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Author Topic:   Explaining the pro-Evolution position
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 241 of 393 (792743)
10-13-2016 8:14 PM
Reply to: Message 239 by Theodoric
10-13-2016 7:52 PM


Re: Mathematics cannot change reality but when done correctly can predict it
quote:
So the reason why dinosaurs can not transform alleles which produce scales into alleles which produce feathers by rmns is that too many genes must be transformed.
How many genes must be transformed to make this change?
What is the limit of the number of genes that could allow the transformation?
I had a link (which is now dead) to a paper where biologists looked at this problem. What they did is looked at the genomes of birds and the genomes of reptiles and tried to determine which genes would need to be transformed to turn scales into feathers. They identified at least eight genes.
Once you get above the transformation of a single gene by a single selection pressure, rmns is stifled. How much is it stifled? Consider the evolution of HIV where only 2 genes are targeted by 3 selection pressures and you have people surviving for decades instead of weeks. If you have huge populations such as seen with Malaria (trillions or more), 2 selection pressures still allows for the emergence of resistance. This happens because with populations this large, the probabilities of double beneficial mutations become realistic. But each evolutionary step means that double beneficial mutation variant must amplify into the trillions as well for the next set of double beneficial mutations. This is why 2 drug therapy will not be adequate for durable treatment of Malaria. 3 drug therapy will be required, in particular with those patients with impaired immune systems.

This message is a reply to:
 Message 239 by Theodoric, posted 10-13-2016 7:52 PM Theodoric has replied

Replies to this message:
 Message 244 by Theodoric, posted 10-13-2016 9:19 PM Kleinman has replied
 Message 265 by Taq, posted 10-14-2016 10:59 AM Kleinman has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 242 of 393 (792744)
10-13-2016 8:38 PM
Reply to: Message 240 by Dr Adequate
10-13-2016 7:58 PM


Re: Mathematics cannot change reality but when done correctly can predict it
quote:
What I think happened is that evolutionary biologists went down a wrong track when the got stuck on the notion of fixation rather than recognizing its amplification which affects the probabilities, not relative frequencies.
Well, fixation is just amplification taken to 100%. And it's easy to work with. It's likely to be a good approximation to math which took the steps from mutation to fixation into effect: such an approximation would start breaking down if and to the extent that beneficial mutations were so common that it's highly likely that a second beneficial mutation will arise before the first one's achieved fixation. Even so, this will not have much qualitative effect: it will still (for example) be the case that evolution goes at a higher rate when there are multiple (soft) selection pressures, because the reasons for that will still apply.
Fixation is not the same as amplification. What if the total population size is 10? If you need a million replications to have a reasonable probability for a particular mutation, that would require 100,000 generations. And fixation is not necessary for amplification to occur. The relative frequencies of the particular variants evolving to a selection pressure can remain constant while the entire population size is increasing. You have to use the number of replications to determine your probabilities.
quote:
You don't have to be the sharpest knife in the drawer to figure out this problem.
That would be kinda my point.
Every week, hundreds of people realize that they can overturn either evolution or the Big Bang with reference to some snippet of math or science they learned in middle school. So far, they have invariably been wrong; and it is easy to see why: if it could be done that easily, it would have been done already.
I actually learned about the multiplication rule of probabilities in elementary school. Maybe evolutionists don't want to think about the multiplication rule for stochastic processes. It kinda gums up the theory of evolution. But it is very useful to understand this if you want to develop durable treatments for cancers and infectious diseases.
quote:
If you did a careful study of a good computer simulation of rmns like Tom Schneider's EV computer simulation and looked carefully at the empirical examples of rmns, its not that hard to see how rmns works.
A good computer simulation actually shows that my math in post #132 is correct. Which is nice for me.
But there is a difference between fixation and amplification. Now random recombination is dependent on relative frequencies of alleles in a population. Now I haven't done the mathematics for rmns for sexually reproducing replicators including recombination. I also think you would have to include Mendelian probabilities in the calculation. I don't think this case will rescue the theory of evolution because the empirical evidence already shows that combination selection pressures stifles rmns (eg combination herbicides) for this class of replicators.

This message is a reply to:
 Message 240 by Dr Adequate, posted 10-13-2016 7:58 PM Dr Adequate has replied

Replies to this message:
 Message 243 by Dr Adequate, posted 10-13-2016 8:54 PM Kleinman has replied
 Message 261 by bluegenes, posted 10-14-2016 9:08 AM Kleinman has replied
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Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 243 of 393 (792745)
10-13-2016 8:54 PM
Reply to: Message 242 by Kleinman
10-13-2016 8:38 PM


Re: Mathematics cannot change reality but when done correctly can predict it
Fixation is not the same as amplification.
Well, fixation is amplification to 100%
What if the total population size is 10? If you need a million replications to have a reasonable probability for a particular mutation, that would require 100,000 generations.
And then fixation, if it occurred at all, would occur quickly, and very likely before any other given beneficial mutation arose. This would be a splendid example of a case where you could entirely neglect amplification as such and just think about fixation.
I actually learned about the multiplication rule of probabilities in elementary school. Maybe evolutionists don't want to think about the multiplication rule for stochastic processes.
The people who worked out the math of the theory of evolution think about the laws of probability quite a lot.
But there is a difference between fixation and amplification.
And a simulation, which has no particular concept of fixation, still produces the same qualitative results as math which uses the concept of fixation, because it is in fact a good approximation.
I don't know why the rest of your post is about recombination.
I don't think this case will rescue the theory of evolution because the empirical evidence already shows that combination selection pressures stifles rmns (eg combination herbicides) for this class of replicators.
Do you have any empirical evidence that this happens when the selection pressures are not hard? You know, cases where the selection pressures aren't us hitting the population with the most virulent poisons our ingenuity can devise?

This message is a reply to:
 Message 242 by Kleinman, posted 10-13-2016 8:38 PM Kleinman has replied

Replies to this message:
 Message 246 by Kleinman, posted 10-13-2016 9:50 PM Dr Adequate has replied

  
Theodoric
Member
Posts: 9076
From: Northwest, WI, USA
Joined: 08-15-2005
Member Rating: 3.7


Message 244 of 393 (792746)
10-13-2016 9:19 PM
Reply to: Message 241 by Kleinman
10-13-2016 8:14 PM


Re: Mathematics cannot change reality but when done correctly can predict it
So your answer to these questions
Theo writes:
How many genes must be transformed to make this change?
What is the limit of the number of genes that could allow the transformation?
is?
I mean really they are simple questions. You have made it very clear that you have figured this all out therefore you must know the answers.
Sorry but that you have a dead link that asserts something doesn't cut it.
Is the answer for the first question 8 or not?
You know the math, are you saying you don't know the answer for the second question?

Facts don't lie or have an agenda. Facts are just facts
"God did it" is not an argument. It is an excuse for intellectual laziness.

This message is a reply to:
 Message 241 by Kleinman, posted 10-13-2016 8:14 PM Kleinman has replied

Replies to this message:
 Message 247 by Kleinman, posted 10-13-2016 10:03 PM Theodoric has not replied

  
Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


(4)
Message 245 of 393 (792748)
10-13-2016 9:47 PM


Bumblebees can't fly...
First, let's look at the physics behind the story. The lift equations for rigid wings are straightforward enough. Bumble-bees are fairly big, weighing almost a gram, and have a wing area of about a square centimetre.Tot up all the figures and you find that bees cannot generate enough lift at their typical flying speed of about 1 ms.
But that doesn't prove that bees cannot fly. All it proves is that bees with smooth, rigid wings cannot glide, which you can show for yourself with a few dead bees and a little lacquer.

So here we have an example of math/physics at work, which shows for a certain set of parameters bumblebees can't fly!
But bumblebees, not having read of this, continue to fly just fine.
So, what does this tell us?
If math and physics professionals model the wrong variables they get the wrong answers, even if all the math is correct.
And, as often is the case, math and physics professionals usually know squat about biology and related subjects. (Increasing one's knowledge of math and physics does not correct this deficiency.)

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
Belief gets in the way of learning--Robert A. Heinlein
In the name of diversity, college student demands to be kept in ignorance of the culture that made diversity a value--StultisTheFool
It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers
If I am entitled to something, someone else is obliged to pay--Jerry Pournelle
If a religion's teachings are true, then it should have nothing to fear from science...--dwise1
"Multiculturalism" demands that the US be tolerant of everything except its own past, culture, traditions, and identity.

Replies to this message:
 Message 249 by Kleinman, posted 10-13-2016 10:12 PM Coyote has replied
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Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 246 of 393 (792749)
10-13-2016 9:50 PM
Reply to: Message 243 by Dr Adequate
10-13-2016 8:54 PM


Re: Mathematics cannot change reality but when done correctly can predict it
quote:
Fixation is not the same as amplification.
Well, fixation is amplification to 100%
Are you sure about that? No more replications after that?
quote:
What if the total population size is 10? If you need a million replications to have a reasonable probability for a particular mutation, that would require 100,000 generations.
And then fixation, if it occurred at all, would occur quickly, and very likely before any other given beneficial mutation arose. This would be a splendid example of a case where you could entirely neglect amplification as such and just think about fixation.
Let's make the example even simpler than that. Let's say you have a population of 10 exact clonal matches. Every allele is already fixed. but you have only 10 replications. To get a million replications with a constant population size over the generations would require 100,000 generations
quote:
I actually learned about the multiplication rule of probabilities in elementary school. Maybe evolutionists don't want to think about the multiplication rule for stochastic processes.
The people who worked out the math of the theory of evolution think about the laws of probability quite a lot.
Of course they do and the earliest paper I know of where the multiplication rule applies to rmns was discussed is Edward Tatum's 1958 Nobel Laureate Lecture. But Haldane and Kimura don't address this aspect of evolution in their models. I have a big advantage over Haldane and Kimura, they didn't have all the empirical evidence of rmns that is available today.
quote:
But there is a difference between fixation and amplification.
And a simulation, which has no particular concept of fixation, still produces the same qualitative results as math which uses the concept of fixation, because it is in fact a good approximation.
You can have amplification without fixation simply by all variants increasing in number yet still maintaining the same relative frequencies and you can have fixation without amplification simply by having all other variants dying out.
quote:
I don't know why the rest of your post is about recombination.
Because the probabilities of random recombination are dependent on the relative frequencies of variants in the population, not the absolute number of each variant.
quote:
I don't think this case will rescue the theory of evolution because the empirical evidence already shows that combination selection pressures stifles rmns (eg combination herbicides) for this class of replicators.
Do you have any empirical evidence that this happens when the selection pressures are not hard? You know, cases where the selection pressures aren't us hitting the population with the most virulent poisons our ingenuity can devise?
The mathematics of rmns is not dependent on the intensity of selection. The question is does the evolutionary trajectory (mutations required) to resistance to the selection pressure(s) change depending on the intensity of selection? The point I think you are trying to make is that if the intensity of the selection is low, amplification will be easier for the remaining variants.
I posted what I thought was a very interesting video of the evolution of resistance of bacteria to an antibiotic. Here's the link to the video again:
Scientists create video of bacteria evolving drug resistance.
I've written to the scientist who made this video and asked that he repeat the experiment with 2 and then with 3 drugs using the same technique of low to high-intensity selection with the combinations. That would give some empirical answer to this question. What I suspect is that if the bacteria are able to evolve resistance to the combinations, it will be much, much slower than to the single drug experiment.
Watch the video and tell me what you think.

This message is a reply to:
 Message 243 by Dr Adequate, posted 10-13-2016 8:54 PM Dr Adequate has replied

Replies to this message:
 Message 248 by Dr Adequate, posted 10-13-2016 10:10 PM Kleinman has not replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 247 of 393 (792750)
10-13-2016 10:03 PM
Reply to: Message 244 by Theodoric
10-13-2016 9:19 PM


Re: Mathematics cannot change reality but when done correctly can predict it
quote:
So your answer to these questions
Theo writes:
How many genes must be transformed to make this change?
What is the limit of the number of genes that could allow the transformation?
is?
I mean really they are simple questions. You have made it very clear that you have figured this all out therefore you must know the answers.
Sorry but that you have a dead link that asserts something doesn't cut it.
Is the answer for the first question 8 or not?
You know the math, are you saying you don't know the answer for the second question?
The web site where this link was posted is a university web site. The web site is still there and I contacted the professor who originally posted the paper and asked for a copy but no response. I'm sure I still have the link and you can contact the professor yourself and see if you can get the paper. What I do remember is that they listed at least 8 genes necessary to be transformed.
If you want, I'll search my older computer and find the link and perhaps you will have better luck finding the paper.

This message is a reply to:
 Message 244 by Theodoric, posted 10-13-2016 9:19 PM Theodoric has not replied

Replies to this message:
 Message 258 by RAZD, posted 10-14-2016 8:52 AM Kleinman has replied

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


Message 248 of 393 (792751)
10-13-2016 10:10 PM
Reply to: Message 246 by Kleinman
10-13-2016 9:50 PM


Re: Mathematics cannot change reality but when done correctly can predict it
Are you sure about that?
Yes.
No more replications after that?
What?
Let's make the example even simpler than that. Let's say you have a population of 10 exact clonal matches. Every allele is already fixed. but you have only 10 replications. To get a million replications with a constant population size over the generations would require 100,000 generations
Why do you mention it?
Of course they do and the earliest paper I know of where the multiplication rule applies to rmns was discussed is Edward Tatum's 1958 Nobel Laureate Lecture. But Haldane and Kimura don't address this aspect of evolution in their models.
They don't address ... the multiplication rule of probabilities?
The mathematics of rmns is not dependent on the intensity of selection.
The math of evolution has to include that as a variable, since it will in fact affect the outcome.
However, large s doesn't necessarily mean hard selection. What I was talking about was whether the selection is hard or soft (which also has to be a variable in the model).
The point I think you are trying to make is that if the intensity of the selection is low, amplification will be easier for the remaining variants.
No ...
What I asked was: "Do you have any empirical evidence that this [i.e. "combination selection pressures stifles rmns"] happens when the selection pressures are not hard? You know, cases where the selection pressures aren't us hitting the population with the most virulent poisons our ingenuity can devise?"
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 246 by Kleinman, posted 10-13-2016 9:50 PM Kleinman has not replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 249 of 393 (792752)
10-13-2016 10:12 PM
Reply to: Message 245 by Coyote
10-13-2016 9:47 PM


Re: Bumblebees can't fly...unless they have big enough engine
quote:
First, let's look at the physics behind the story. The lift equations for rigid wings are straightforward enough. Bumble-bees are fairly big, weighing almost a gram, and have a wing area of about a square centimetre.Tot up all the figures and you find that bees cannot generate enough lift at their typical flying speed of about 1 ms.
But that doesn't prove that bees cannot fly. All it proves is that bees with smooth, rigid wings cannot glide, which you can show for yourself with a few dead bees and a little lacquer.

So here we have an example of math/physics at work, which shows for a certain set of parameters bumblebees can't fly!
But bumblebees, not having read of this, continue to fly just fine.
So, what does this tell us?
If math and physics professionals model the wrong variables they get the wrong answers, even if all the math is correct.
And, as often is the case, math and physics professionals usually know squat about biology and related subjects. (Increasing one's knowledge of math and physics does not correct this deficiency.)
Early in my career, I worked in the aerospace industry. We had a saying "Put a big enough engine on anything and you can make it fly". I assure you that I have enough training in microbiology, biology, organic chemistry, biochemistry, genetics,... to understand rmns. You show me your degrees and I'll show you mine. And I'm pretty sure I've had a lot more training in mathematics and physics than you.

This message is a reply to:
 Message 245 by Coyote, posted 10-13-2016 9:47 PM Coyote has replied

Replies to this message:
 Message 250 by Coyote, posted 10-13-2016 10:28 PM Kleinman has not replied
 Message 255 by Rrhain, posted 10-14-2016 4:39 AM Kleinman has replied
 Message 256 by Pressie, posted 10-14-2016 7:19 AM Kleinman has replied

  
Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


Message 250 of 393 (792753)
10-13-2016 10:28 PM
Reply to: Message 249 by Kleinman
10-13-2016 10:12 PM


Re: Bumblebees can't fly...unless they have big enough engine
You may have more training in math and physics than I do, but you are making the classic creationist "magic bullet" mistake we see so often here. (And I do have a few degrees hanging on my wall. Well, actually, they're stuffed in a drawer somewhere.)
A little knowledge is a dangerous thing, but a lot of knowledge in a very narrow and largely unrelated field lets you put the silver dagger in the heart of the theory of evolution, eh?
You are about the ten thousandth person to try this, or so it seems. So far none has succeeded.

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
Belief gets in the way of learning--Robert A. Heinlein
In the name of diversity, college student demands to be kept in ignorance of the culture that made diversity a value--StultisTheFool
It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers
If I am entitled to something, someone else is obliged to pay--Jerry Pournelle
If a religion's teachings are true, then it should have nothing to fear from science...--dwise1
"Multiculturalism" demands that the US be tolerant of everything except its own past, culture, traditions, and identity.

This message is a reply to:
 Message 249 by Kleinman, posted 10-13-2016 10:12 PM Kleinman has not replied

Replies to this message:
 Message 251 by dwise1, posted 10-14-2016 12:22 AM Coyote has seen this message but not replied

  
dwise1
Member
Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 251 of 393 (792757)
10-14-2016 12:22 AM
Reply to: Message 250 by Coyote
10-13-2016 10:28 PM


Re: Bumblebees can't fly...unless they have big enough engine
"If you can't dazzle them with your brilliance, then baffle them with your bullshit."
I think that that describes the IDists quite well. The inability of YECs to understand even the most basic science, coupled with the inability to quote any scientific source accurately, makes it child's play to shoot down the vast majority of typical YEC arguments; they fall apart immediately upon examination.
OTOH, the IDists are experts at bullshit. They will throw all kinds of technical chaff at you to hide what they are really doing. Their bullshit is truly of a much higher quality than that of other creationists.

This message is a reply to:
 Message 250 by Coyote, posted 10-13-2016 10:28 PM Coyote has seen this message but not replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 252 of 393 (792758)
10-14-2016 12:24 AM
Reply to: Message 235 by Kleinman
10-13-2016 6:28 PM


Re: Mathematics cannot change reality but when done correctly can predict it
quote:
That's right. So then how does this change the mathematics
Obviously if reality differs from the model, the model is wrong and must be changed. Whether you consider that a change in the mathematics or not is irrelevant.
quote:
I've done the recombination calculation alone to study why recombination does not have a significant effect on the evolution of drug-resistant HIV.
You aren't much of a mathematician if you think that examining one special case is enough to demonstrate a claim about the general case.
quote:
The empirical evidence already is clear that rmns is not significantly altered by sexual reproduction. Combination herbicides are already known to impair the evolution of herbicide-resistant weeds. There are other examples as well.
Again you insist on talking about a set of very similar special cases but claim to have a generally applicable model. You might wish to consider how it is that combination therapies work, yet multiply-resistant bacteria are such a problem. That might lead you to a useful insight in understanding why combination therapies work.

This message is a reply to:
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dwise1
Member
Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


Message 253 of 393 (792761)
10-14-2016 1:50 AM
Reply to: Message 237 by Kleinman
10-13-2016 6:44 PM


Re: Mathematics cannot change reality but when done correctly can predict it
With all due respect, but did nobody else notice that "little man's" (ie, Kleineman) source was Tom Schneider's EV computer simulation, which I was only able to find on creationist sites.

This message is a reply to:
 Message 237 by Kleinman, posted 10-13-2016 6:44 PM Kleinman has not replied

  
Rrhain
Member
Posts: 6351
From: San Diego, CA, USA
Joined: 05-03-2003


Message 254 of 393 (792763)
10-14-2016 4:34 AM
Reply to: Message 245 by Coyote
10-13-2016 9:47 PM


Re: Bumblebees can't fly...
Coyote writes:
quote:
If math and physics professionals model the wrong variables they get the wrong answers, even if all the math is correct.
This is a lovely story, but it's just that: A story. You cribbed your story from Physics World and you should have kept on going:
So how do bees fly then? And why do they need to flap their wings while jumbo jets don't? These turn out to be very interesting questions that reveal a lot of physics. Jumbo jets have fixed wings because their wing area and speed are large enough to satisfy the lift equations for flight. But the small wings on a bumble-bee are much less efficient. Coupled with low speeds and the high drag on a wing when flapping, it might appear, at first glance, that insects cannot fly and that most birds can't get off the ground either.
It goes even further, talking about the way the eddies off the wings generate a secondary lift, for example.
quote:
And, as often is the case, math and physics professionals usually know squat about biology and related subjects.
Or, math and physics professionals are smart enough to understand that if you already know the answer and your model doesn't actually spit it out, that means the model is wrong and you need to do more work.

Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

Minds are like parachutes. Just because you've lost yours doesn't mean you can use mine.

This message is a reply to:
 Message 245 by Coyote, posted 10-13-2016 9:47 PM Coyote has not replied

Replies to this message:
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Rrhain
Member
Posts: 6351
From: San Diego, CA, USA
Joined: 05-03-2003


Message 255 of 393 (792764)
10-14-2016 4:39 AM
Reply to: Message 249 by Kleinman
10-13-2016 10:12 PM


Re: Bumblebees can't fly...unless they have big enough engine
Kleinman writes:
quote:
And I'm pretty sure I've had a lot more training in mathematics and physics than you.
And I'm sure you haven't. After all, you haven't answered any of my questions about mathematics:
You have a standard deck of 52 cards. You randomly choose a card.
What is the probability of having drawn the Ace of Spades?
What is the probability of having drawn an Ace?
What is the probability of having drawn a Spade?
What is the probability of having drawn a black card?
What is the probability of having drawn a card?
What is the probability of having drawn the Ace of Spades given no information?
What is the probability of having drawn the Ace of Spades given that it is an Ace?
What is the probability of having drawn the Ace of Spades given that it is a Spade?
What is the probability of having drawn the Ace of Spades given that it is a black card?
Suppose you have a single-gene trait with two alleles with perfect dominant/recessive expression. If you are homozygous for dominant allele or heterozygous, you display the dominant trait. Only if you are homozygous for recessive allele do you display the recessive trait and you always do if you are homozygous recessive. Suppose the current rate of recessive display is 1-in-1,000. Suppose that those who display recessive trait are sterile and cannot reproduce while those who display dominant trait (either homozygous dominant or heterozygous) have no difference in reproductive capability.
How many generations would need to pass in order to reduce the appearance of recessive trait from 1-in-1,000 to 1-in-1,000,000?
To help you start: What is the value for p? What is the value for q?

Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

Minds are like parachutes. Just because you've lost yours doesn't mean you can use mine.

This message is a reply to:
 Message 249 by Kleinman, posted 10-13-2016 10:12 PM Kleinman has replied

Replies to this message:
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