Thank you! Unfortunately I live in the UK and going all the way to the States to settle an internet debate is taking things just a bit too far. I draw the line at going to bed late 
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Truth be told I look forward to going in the field so I can get away from internet squables
Nothing like a week or so sleeping out without a roof to put me back in touch with the real world.
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Yes, but with common ancestry, humans weren’t around to increase reproductive success of plants that had beneficial traits. I’m still learning what a beneficial mutation is, but Sanford seems to be more encompassing of what a beneficial mutation could be because he describes it as useful and not just related to reproductive success, when you would describe it as both to create common ancestry?
I figured y’all may miss the point I see.
One beneficial mutation in 10,000 to 1,000,000.
Again here:
Basically, positive changes + reproductive success are not high enough for natural selection to create all of the life we see today via common ancestry.
Yes, humans have created beneficial crops this way, but there are only dozens. Nature cannot create thousands upon thousands. We had to have diversity and design built-in.
Anyway, I better keep reading the rest of the book so I can get better at arguing this 
No, actually, you seem to be avoiding the point. The examples provided concerning the utility of mutagenesis in crop improvement related to this quoted statement of Sanford’s:
However, from all this effort, almost no meaningful crop improvement resulted. The effort was for the most part an enormous failure, was almost entirely abandoned. Why did this huge mutation/selection experiment fail - even with a host of PhD scientists trying to help it along? It was because even with all of those billions of mutation, there were not significant new beneficial mutations arising. The exception proves the point. Low phytate corn is the most notable example of successful mutation breeding.
Sanford here is saying all those decades of using chemical mutagens and irradiation produced one - ONE - success. He’s wrong. Period.
That is the point. Short, succinct, simple.
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No, he gave other examples of how it produced other successes. See below.
So what? Rather than humans picking and choosing plants to cultivate for desirable traits, in the wild the effects of mutations on the plant’s ability to survive and reproduce would be determined by the environment of the plant. This is totally basic natural selection.
I don’t think it’s a particularly complicated concept. The traits of organisms affect their ability to survive in their environment, and their ability to reproduce. If a mutation has a positive effect on this ability (it doesn’t matter how it accomplishes this) then it is a beneficial mutation by definition.
Yes and that’s one of the problems with Sanford’s whole GE idea, because there are many good measurements that show that beneficial mutations increase over time so much that they really do increase the survival and reproductive success of the organism, so when this happens Sanford changes the definition of beneficial mutation away from having to do only with reproductive success and now also demands that the mutation does things like “increase the integrity of information in the genome”(a term he doesn’t define in a way that can be measured).
That sounds like a large ratio. But can you show that that ratio can’t result in continuous fitness increase? Sanford has tried, but when he does, his models contradicts real-world measurements. So he makes up an excuse for why (and it’s there in your quote below).
Now, let’s try a really simple calculation here just to sort of get a handle on whether the number you quote indicates any sort of problem at all. Let’s just go with the number you supplied.
Even if 1 in 1 million mutations are beneficial, how many mutations happen in a whole plant population every generation? If there are 10 billion individuals in a population of some plant in nature(think of a plant like Dandelions, how many total dandelions exist, and how many seeds does each new dandelion produce every generation?), and if each individual in that population has 2 offspring every generation (and that on average 1 of them dies so the population stays at a constant size), and that every new such plant “born” every generation has 20 new mutations, how many mutations in total are there to select among? Well let’s see, 10 billion times 2 times 20 mutations = 400 billion mutations. Even if only 1 in 1 million mutations are beneficial, then there are 400 000 new beneficial mutations occurring every generation.
And that’s those “very rare beneficials that have major effect”. Those “anomalies” that humans were able to find and select, right?
But they’re not exceptions. They exist frequently enough to be selectable(how were humans able to find and select them if they’re not selectable?), and to increase the survival and reproductive success of the organism. So they are not at all “anomalies”. They’re demonstrably real. And humans were able to find many of them in just a few decades of experiments(see that list again). In the real history of life, plants have existed on Earth for not far off from a billion years.
Now notice the crucial thing. What Sanford does next is to change the definition of beneficial mutations away from fitness(fitness is the term for survival and reproductive success). This is EXACTLY where a sleight of hand takes place. Sanford knows that in real-world experiments, reproductive success can be shown to go up continously(it can be shown that the effect of beneficial mutations, which he insist are so rare as to be anomaloous, nevertheless increase the survival and reproductive rate of living organisms), something he thinks shouldn’t be possible.
So what does Sanford do? He makes up an excuse! He redefines fitness to means something other than just reproductive success. Now he also wants mutations to “increase the integrity of information in the genome”, and/or result in “new capabilities/new functions”, all at the same time.
But there is just no requirement that a mutation must have all of these effects simultaneously for life to evolve. Some mutations can be fitness increasing without creating new functions. Some mutations can create functions without increasing fitness. Some mutations can increase information while reducing fitness. All combinations of these are possible. So Sanford is simply wrong to say that for something like the evolutionary history between single-celled life all the way to multicellular organisms like fish and birds, mutations must simultaneously show all these effects. But why must a mutation simultaneously do all those things? Can’t some mutations increase fitness, other mutations increase information, and still other mutations occasionally result in a new function? And that, as long as there have occasionally been some of each, there is no difficulty with with observing that over some very long period of time in the history of some lineage of organisms, some time fitness has gone up, other times it has gone down, some times functions have been gained, other times functions have been lost, some times information has been gained, and some times it has been lost? There is just no requirement that these three different measures must always follow each other. Simply from the standpoint of logic alone, Sanford’s thesis does not hold up.
But Sanford hasn’t shown that at all.
But why not? It seems to me the simple back-of-the-envelope calculation I did above shows that even in one single generation of plants with a large population size, there is an enormous wealth of potentially beneficial mutations to select among.
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And there we have it, Sanford commits the switcheroo. Now he wants the mutation to do something special besides also increasing reproductive success. But why must it do so? Why can’t one mutation increase reproductive success here and there, and then perhaps more rarely, other mutations result in new functions? And occasionally mutations increase information? Why is Sanford demanding that the mutation must have all these effects simultaneously?
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Sanford clearly doesn’t consider these to be beneficial - that’s why he slips in the adjective “dysfunctional”. He’s quite completely wrong in his representation of this field. We have seen some examples already, and I could fill out several hundreds of lines with more descriptions of things Sanford implies do not exist.
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Or to, say, make a plant more attractive to pollinators, or a bird more attractive to potential mates…
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Actually, nature can. For example (to stay in Sanford’s wheelhouse), we see in the wild and in the cultivated field an endless arms race between pathogens and plant. This arms race entails repeated rounds of new beneficial mutations in the pathogen (to give rise to a new effector protein) followed by new beneficial mutations in the plant to yield receptors that specifically recognize these newly-evolved effector proteins. Without fairly rapid (in evolutionary time scales) origination of new receptor specificities, plants would have gone extinct many many millennia ago.
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But perhaps you are missing the point here.
If a population is well adapted, there will be few beneficial mutations. If a population is poorly adapted, there will be more beneficial mutations.
Or look at an analogy. If you are at the top of the mountain, then every step will tend to be a step down. But if you are part way up, then some steps will take you higher.
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You’re irresponsibly conflating what Sanford claims to be true with what is true.
Please stop, as you’re obviously just parroting, not bothering to examine any evidence for yourself.
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That’s not his GE idea. It’s that the deleterious and neutral mutations far outweigh any beneficials even while survival increases.
I don’t think he’s demanding it; he’s exposing that it isn’t the case, and it must be the case for common ancestry of all living things to be true.
And you have the research that shows that these plants don’t lose other receptors, that are now unused, at the same time?
Yes - how else did the we get the complexity of the genome compared to other animals we shared a common ancestor with?
I’ll try to get a lot farther in the book tonight. I feel silly arguing from a few chapters in a topic I’m new at, so I’m probably getting a few things wrong. But it’s still odd that his main idea is not understood as far as I can tell.
[quote=“thoughtful, post:167, topic:12338”]
Yes, we do. (We = the plant biology community.)
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I really was asking for you to link the papers
I know that’s not his idea, but it’s one of the problems with his idea. That is how he defends it when the real world refuses to conform to his idea.
No, it is simply not correct that it “must” be the case for common ancestry of all known life to be true. I just explained why that isn’t necessary.
By complexity going up more than it has gone down in some lineages, without that necessarily having tracked along with fitness, or genetic information too. So you can get fitness going up some times, while complexity remains the same, and information decreases a bit. And then they can change around so fitness stays the same or goes down a bit, while complexity goes up a lot, and genetic information increases by a small amount. And every other possible mix of these.
By simply having uncorrelated fitness, genetic information, and complexity. More complexity or more information isn’t always better for survival.
We can see simply from the standpoint of logic, by using our ability to reason, that these do not have to match up all the time. Some times, “less is more”. It depends on circumstances. There are circumstances where being less complex is advantageous, it depends.
Just a simple figure I’ve drawn to explain the principle of it:
They are three different measures, fitness, information, and complexity. A bacterium can have many, many more offspring than you can, while you are more complex. And the environment you live in can change so some of your traits that used to be beneficial can become deleterious, and vice versa.
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You’re asking for hundreds and hundreds of papers. My recommendation - follow the google path to plant defense receptors, and also plant pathogen effector proteins, and start poking around. I expect that basic wiki pages will be good enough for starters.
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The blog post was mine. I will admit that I’m not a professional geologist and I haven’t visited the rock formation in question (though I would like to sometime). My university degree is in physics and I work as a software developer.
I fully understand @faded_Glory’s frustration here. There does need to be some sort of a bar to meaningful and honest discussion about science — there are far too many Dunning-Kruger types out there who think they know more about science than “secular scientists” despite having studied English Literature, Classical Civilisation or International Relations and not having set foot in a laboratory since they were at school. And there is a limit to how much I can say about claims such as this one, without actually visiting the rock formation in question, taking samples, performing analyses, and applying the necessary expertise.
But that limit is not nothing. There are many of us who are scientifically literate Christians but who aren’t necessarily experts in one particular facet of the debate, but nonetheless have to draw informed conclusions about it, not least so that we can advise our pastors and fellow believers what to make of it all. We have to go with what data is available to us, the general principles of science that we do understand from our education and professional experience, and basic rules of critical thinking in order to form a decision about which experts we can consider credible and which we can not.
Herein lies the problem: @faded_Glory is setting the bar too high. My post was one of a series addressing the question, what should I, as a scientifically literate Christian, make of Answers in Genesis’s “ten best evidences for a young earth”? It is a pretty diverse set of claims, covering everything from sedimentology to soft tissue preservation to astronomy and cosmology, and there can be few if any scientists alive who have conducted field studies of their own in all ten areas.
That’s why I made the analogy that I did with FizzBuzz. Besides filtering out total incompetents, it is a test that can be understood and administered even by people with very limited programming experience. You don’t need to know how to configure a Kubernetes cluster (or even understand what that means) in order to identify a non-FizzBuzzer, and in the same way, you don’t need to go on field trips or conduct advanced laboratory analyses to tell that when someone claims that a rock formation isn’t cracked when cracks are clearly visible in photographs of that rock formation, they’ve failed the geological equivalent of FizzBuzz.
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OK. The addition of genetic information you propose would refute GE. Can you show it has been observed?
I looked and the first one I clicked on seems to confirm GE.
Our lab has been interested in identifying novel negative regulators of plant immunity (Gao et al., 2008). Loss-of-function mutations in these negative regulators would yield mutants with enhanced pathogen resistance and dwarfism that is usually associated with strong resistance phenotypes. Very rarely, gain-of-function mutations in positive regulators in the same pathways would yield mutants with similar phenotypes, such as in snc1 (Li et al., 2001).
Thank you for explaining where you are coming from. I certainly do appreciate well-founded attempts at debunking false claims (especially when they are in my own field!). I don’t move in creationist circles, so I won’t claim to understand what the best way is to overcome the inbuilt resistance to accepting proper science if that conflicts with their beliefs. We see this resistance every day here and on other discussion sites. I also see that all the patient explaining and arguing that so many people do seems to have very little effect on entrenched positions.
So what to do? My view is that all we can do on our side is rigorously stick to the real science. Science is our strength and we should use it to the full. We should also make sure that we don’t risk damaging the reputation and integrity of the science. That means that we probably should leave detailed explanations to the actual experts, even though we are chomping at the bit to have a go ourselves. Sometimes it is better to back off a little and let more qualified others do the explaning.
Peaceful Science is a great place because many of the commentors indeed are specialists in their own field, and reading what they have to say is of immense value and importance. Myself, I read many of the threads on actual evolutionary biology but I rarely if ever post a comment there - because I’m not an evolutionary biologist and I am simply not qualified to participate at that level.
Perhaps a good role for a non-expert who wants to be involved would be to hunt for published scientific counter-arguments and present those as a counterweight to dubious claims, rather than try to construct those counter-arguments ourselves. Even then we should be very careful not to make innocent mistakes in presenting that science - if in doubt, leave it out, that kind of thing.
The trouble with the geoscience literature is that there is no equivalent to PubMed. The vast bulk of papers are behind paywalls and won’t be accessible unless you are academically affiliated. What is published on the Internet is just a tiny fraction of the available literature, and what there is can be a real hit-and-miss affair in terms of quality. That leaves even the experts without a lot of ammo when it comes to Internet debates. This can lead to proliferation of false and pseudo-science by the unscrupulous, but until something changes on the literature accessibility side, it is what we’re stuck with unfortunately. I just don’t think that well-meant but essentially less informed pushback from non-experts is a substitute (even though the efforts are appreciated!).
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