Can you describe it’s nature, or a range of values where it tends to lie? Like, for example, the border between red and yellow lies somewhere in the middle of the “orange” range, between colors that are yellowish orange, like the color of cheddar cheese, and reddish orange, like the color of campfire coals.
I’m not trying to think in terms of black and white. Maybe I’m not explaining myself very well. I’m trying to say that the limit is not the point at which things start dying, but well before that. In fact, in order for purifying selection to begin to operate, the decrease in a trait doesn’t have to decrease below replacement level, its just that the relative difference in fitness, that is, the selection co-efficient, has to be large enough that it stands out against the background of variation. I am saying that as scarcity comes in to play, the relative value of any given deleterious mutation moves on a continuum. The value of s, in any given situation is not static, it is going to change given the context of the other mutations extant in the organism. This is widely observed in a number of studies according to
I will clean up my language. According to Ohta and Kimura’s probability of fixation formula for nearly neutral mutations, the probability of fixation for a nearly neutral mutation is going to be dependent upon its selection co-efficient. As the selection co-efficient exceeds -1/(4(effective population)) the probability of fixation shrinks asymptotically to zero. In circumstances where progressive deleterious mutations affect genetic modules which in turn influence a trait, I put it to you that the relative fitness of the carriers of that trait, as measured by the magnitude of that negative selection co-efficient for that deleterious mutation will increase in magnitude as the mutations affecting genetic modules for that trait accumulate, until it reaches a point where subsequent mutations affecting such modules have selection coefficients that exceeds -1/(4*(effective population)), and as a result, the chances that such a genetic mutation will reach fixation within a population will drop to very near to zero. Isn’t that true?
“The genetic theory of adaptation: a brief history” by H. Allen Orr reviews a number of examples.
I can’t understand why it would not be true that if a beneficial mutation has a given s co-efficient that the back mutation of that same sequence to the way it was before would not equal the exact same co-efficient but with the opposite sign (negative versus positive). I appreciate an explanation of this, because I thought it was intuitive. Maybe that was my mistake.
It’s not an observation that @Giltil has made, which was my point.
Agreed.
Let’s see what Gil himself says about that, if anything. I’m predicting only another Nigel Tufnelesque response, if any.
Exactement, yet Gil seems to be utterly oblivious to that blatant contradiction.
Yup, that’s what he’s essentially saying while ignoring the existence of intraspecies variation. It also blatantly contradicts @gpuccio’s assumption regarding functional information.
Yup, and yet we have objective observations that show both of Gil’s self-contradictory assumptions to be false!
It’s amazing.
Another beautiful summary. I don’t think Gil can consider the contradiction.
That’s why assumptions and predictions of ID hypotheses must always be (falsely) presented as objective observations, while rejecting the scientific method–it is necessary to maintain the compartmentalization.
From our perspective as biologists, you certainly come across as doing so:
“if the trait affects survival, being bad enough at it is going to kill you”
Selection works at the level of reproduction. It does not work at the level of survival, except survival through reproductive age. This is an enormous fault in your understanding of evolutionary biology.
No. Just think of a model of strictly additive effect. Any additional mutation diminishes fitness just a tiny bit, insufficient to overcome drift. At some point the average reproductive success of the population diminished past replacement level, but even this is subject to considerable stochastic variation. It’s all fuzzy, and even the fuzziness is fuzzy. There is no line, just a continuum.
True. But does it ever reach that point? And you shouldn’t think about “a trait”. It’s whole organisms and whole genomes that have fitnesses. It’s a genetic load argument. Does epistasis even operate on the whole-genome level? I have doubts. And even if you adopt this model of increasing epistatic effect, can you show that individual mutations become subject to selection before the population’s absolute fitness reaches a dangerously low level?
Yes, if the attendant assumptions are correct.
Paywalled. Based on the abstract I’m not sure that the cases are comparable, or that the large effect of an initial mutation arises because it’s the first.
Sure, but that would require a series of exact reversals, and would require that the magnitude of beneficial effects of mutations depends solely on where in a temporal series the mutation lies. Perhaps Orr clarifies this in his full paper.
It’s an observation that I mentioned to him and that he then worked some simple math on. Not a problem.
I see I need to be more careful with my language. In context, I thought it was clear that I was talking about how an incremental step in respect of an important function (the loss of which could be fatal) could be quantified in popgen terms as a decrease in the selection coefficient.
Here is the quote in context:
My understanding is that the selection coefficient embodies in itself the idea that a deleterious mutation is going to decrease the number of offspring a person has which will themselves survive to reproductive age, and so I thought that by referring to the selection coefficient I was communicating that I understood that it is not about whether any one individual lives or dies. In this context, I have always argued that what matters is the resultant effect on the probability of the mutation reaching fixation, which is dependent on the strength of the selection co-efficient (and the population size). The core of my argument here is that as these deleterious mutations pile up with respect to a given trait, the marginal effect of each of them is going to increase, such that at some point the difference in a new mutation will be visible to selection to the extent that such a mutation will be unlikely to reach fixation in a population through drift. That’s the limit I’m arguing exists.
I’m saying that as you begin to run low on surplus capability with respect to a given trait, each marginal decrease in function has a greater effect than the last, and at some point that marginal decrease is sufficient to make it visible to selection in a manner sufficient to make it unlikely that it will reach fixation. As I have said, it is the fact that the population size is so large that makes this selection so efficient in the case of humans. For a newly arising mutation to reach fixation, it will have to spread across 8 billion humans. That will take a lot of generations, and every generation there is a chance that this little change will make a difference in terms of the number of children one of those descendants has. The difference caused by this incremental change only needs to be large enough that it stands out against the base level of variation in the population. Once it does, the chances of fixation for such a newly acquired deleterious mutation, goes down. At this point that trait will stabilize at mutation selection equilibrium, and any significant number of further deleterious mutations in respect of that trait will not reach fixation in the population.
This is just my little pet theory, and as you know, I’m not the one with a PhD in evolutionary biology, you guys are. So I am humbly presenting this as my understanding of the science to you, and I welcome you to correct me. I am sure there are going to be many flaws in my understanding of evolutionary biology. I’m still just learning.
Once again, I appreciate you all taking the time to set me straight about this stuff. If I seem stubborn and willful, that’s probably just a character flaw rather than an effort to remain ignorant or be “right”. I’m happy to be wrong here, with you guys, and then be right when I talk to the creationists.
In my mind, this is going on with all of the different traits all over the world, all at the same time, but in terms of the epistasis, i kind of assumed that they only really operated on a trait by trait level (like all of the genes for folding a given protein could have an epistatic effect, but they would not interact with genes for regulating pairwise interactions between residues in different secondary structure elements in some other protein, for example) however, I don’t have anything to back that up, that was just what I assumed.
This said, I feel like mathematically it should be true that individual mutations should become subject to selection before a population’s absolute fitness reaches dangerously low levels, at least for large populations, because the strength of selection is so strong. I don’t know how small a population would need to get before it became possible for real damage to occur, or how many “traits” could operate simultaneously before it became problematic.
I feel like it should be possible to test this, and/or show that individual mutations become subject to selection before a population’s absolute fitness reached a dangerously low level somehow… maybe by using some computer modeling, but I wouldn’t know the first thing about programming such a model.
What model would I even use? How would I go about doing this? I feel like I just talked myself into a science project that I don’t know how to do!
I don’t think you need to do a project. Nature already has. We know that GE doesn’t happen except possibly under very extreme conditions because if it did, everything would be extinct by now. You don’t need another argument against it. GE relies on a recent creation of species with perfect genomes, and even then species with fast generations all ought to be gone by now. But the best way to attack GE is to attack YEC. (Note that the Flood doesn’t reset GE either.) If life is old, GE doesn’t apply.
@MrAnderson - John makes an important point here. Creation Science isn’t science, it’s apologetics. If you get deep into the weeds explaining just how the science works, then there is a problem …
That problem happens when someone accepts the burden of defending the science against a non-scientific argument. This is generally a recipe for endless argument, and I’m sure you know what I mean. It’s good to know the science and how to defend it, but whenever possible you should put the burden of proof on the person asking the question. For instance, a consequence of GE should be that rapidly reproducing species should have gone extinct long ago, but we still have mosquitos.
Your mathematical intuition is correct. If we simplify fitness to a single continuous variable, then we can represent fitness in a population as a probability distribution. Mutations add new levels of fitness to this population, which must increase the variability. In statistical terms this is increasing the Variance of the population.
If the difference in fitness between the most/least fit members of the population is too small to be acted on by selection in the original population (a premise of GE), then adding new mutations will increase that difference until it reaches a threshold where selection for fitness will occur.
A hidden assumption of GE is that all individuals are identical (uniform with respect to fitness), and/or the statistical variance in fitness is small (or zero). In terms of math, it presumes that evolution happens to (identical) individuals, which is wrong; evolution happens in populations.
I sometimes get myself in trouble by oversimplifying biology, but the underlying math favors a situation where selection for fitness must be possible.
I honestly never thought I would even get that far. Even a highly qualified conditional approval from someone of your stature is kind of a big deal to me as someone who has no business even splashing around near the deep end of the pool.
I think you are essentially correct, but the example is overly complicated. Let me think about a way to state your example in a way where we can write down the math.
Oh deer. My advice (also seemingly shared by others here), don’t feed the troll. If you are looking for someone with intellectually honesty, Donny isn’t your guy. Don’t waste your time.
Many years ago, I tried to have a conversation with him to discuss his claims point by point. Of course he tipped his fedora hat and challenged me to a debate several times, like the annoying debate bro that he is. I tried to convince him that it would be much more productive to converse on a forum in a written format, so we can take the time to examine the evidence, which you can’t do in live debates. Or you have to be prepared for every point your opponent may bring up, but that’s often not the case. And not the mention that you often don’t have enough time to respond to every single point being brought up. After several attempts to persuade him, Donny eventually agreed to do a written discussion on the condition that I first made a post addressing one point (the claim that the H1N1 virus was affected by genetic entropy). Unsurprisingly, after I posted my response on the forum, he broke his promise and refused to do a written discussion. Instead, he started to respond to my rebuttals with hour(s) of live stream tirades, kept challenging me to live youtube debates (again), and increasingly became more belligerent to the point of outright admitting that he is NOT interested in having an honest and productive conversation. He just wants to posture and show-off in front of his audience. Here is just a sample of the type of replies I received from him:
Would you like me to set up a debate between you, Jeremy and myself? You can bring Ration. If not then thats fine but Im not joining your blog Ive looked over it and the arguments are sad. I will continue making videos debunking anything you put in it. I don’t do this for you and the other BIASED atheists. I’ve chosen to do this to show FELLOW brothers in Christ that you evolutionary heavyweights of YouTube are not as smart as you think. I am enjoying this too much. Joining a forum is not something I am interested in. Debates are quick and easy and people can see both sides and come to a valid conclusion on whose side is better in light of the evidence. You have all fallen one by one, Jackson, RJ & the rest of the crew. You guys should retire because theres a new sherrif in town. This is Standing For Truths territory now. And Jeremy wiped the floor with you guys. You vs Jeremy on Haplogroups. Bring it. Chicken.
Yes… calling me a chicken AFTER back pedaling on an agreement to discuss in a written format. The hypocrite.
But… if you really want to debate this cartoon character, here are my thoughts on the following:
That’s not necessary. You need to point out that an analogy doesn’t suffice as evidence. He doesn’t get to throw out an analogy and expect you to prove him wrong. He is the one who need to back up his claims with actual substance. The substance (evidence) is what you need to respond to. You could explain why the analogy is wrong, but it’s just an analogy at the end of the day. Even showing that his analogy is dumb wouldn’t disprove his claim. He can just come up with another stupid analogy to waste your time on. I would suggest to avoid being mired in analogies and cut straight to the chase and demand for anything which demonstrate that genetic entropy is actually a thing.
It’s also vitally important to point out that he needs to define the concept of genetic entropy in a manner that leaves no room for ambiguity. He has to answer questions such as: What would you expect to see in a population of organisms that is affected by genetic entropy in contrast to one that isn’t affected? Decline of fitness, or something else? Or can we tell the difference via genome sequencing. If so, how exactly? What is the counterfactual(s) that we can observe or measure?
Often, when faced with such questions, they will quickly distance themselves from observable phenomenon, such as ‘fitness’. We know of populations that maintain fitness, and in some fitness increases, which doesn’t work out well for them if you use this as a measure of ‘genetic entropy’. At this point, they will likely muddy the waters by saying that genetic entropy is a decrease of “genetic information” or just “information”; without ever defining it or specifically provide a way to test whether this “information” is increasing, decreasing, or remaining constant. When that happens, don’t let him off the hook. Keep pointing out that if they don’t provide a way to test genetic entropy, then their claim has no basis to begin with. This will be a case of “Not Even Wrong”.
@MrAnderson There is something missing here: Sanford suggests a threshold for difference in Fitness, and selection “cannot see small differences.” I don’t see any easy way of doing this with categories of students; we really need a continuous scale of fitness where we can specify a threshold.
Calculations for this could get messy, but I might have a trick under my bell-curve shaped hat.
More tomorrow.
The last debate I think I scored some good points (see post 1 for the link), but I didn’t go for the kill like I did for Hovind.
Right now I think Donny is still in “honeymoon” mode because he wants to me to engage on his channel, but I am wary that the turn is coming and I have seen some of the ugly side of him in his interactions with others.
If he runs out tries to obfuscate, I’ll run him down. That’s my specialty, but I don’t want to get caught out on the science, which is why I’m on here leaning on you guys. Load me up with your best arguments and I can fire the big guns.
Oh, I almost forgot to mention another example of Donny’s blatant intellectual dishonesty.
A while after I tried to start a productive conversation with Donny, I began watching his videos on his channel. These videos were voiced (and also probably edited) by someone who calls himself ‘raw matt’. They were amazingly bad. It’s almost impressive to be so wrong without doing it on purpose. Correcting every mistake would take too much time. So, instead I would watch a new video for a few minutes, quickly point out the most obvious and egregious mistakes in the comment section, and move on with my day. On one occasion, one of these videos was deleted the day after I commented. On the same day, a new video was uploaded with the same content except for the parts that contained the mistakes I called out. These were quietly deleted. They provided no explicit reason for why they did this. They don’t even inform their audience about the mistakes that they edited out. This shows they only care about their reputation and not suffer any minor embarrassment from correcting mistakes, even if it means keeping their audience in the dark.
This wasn’t the only time something like this happened. Lucky for me, I took the liberty to download the video before it was taken down and I could compare the original with the updated version. Here is the video that I made documenting the full indecent:
@MrAnderson
Suppose that fitness has a normal distribution N(\mu,\sigma^2), and we want to compare two members of the population (X_1, X_2) for relative fitness. The difference (Y) of the two also has a normal distribution,
Y = X_2 - X_1 \sim N(X_2 - X_1, 2\sigma^2)
The probability that X_2 is greater than X_1 can be calculated as
Calculating the probability that any two observations will differ by at least 2 is simply twice this amount (just like calculating a two-tail p-value). For the difference k=x_2-x_1,
Now in Sanford’s terms, if selection “cannot see” the difference in fitness levels below a given threshold, we can calculate the proportion of the population with differences greater than that threshold. The example shows the calculation for a threshold of 2 standard deviations, and we can interpret this to say about 25% of the population has fitness high (or low) enough “to be seen” by selection.
Note: The situation where fitness is effected by the cumulative effect of many small mutations (deleterious or otherwise), is exactly the setting that leads to normally distributed random variables. I think it is very reasonable to model fitness as a normally distributed variable.
NOW we can apply this to the students example using a continuous variable for fitness. There is still some work to do, but this shows how to do the basic probability calculations. We will need the Truncated Normal distribution too. Doing this for multiple years of students may require a numeric simulation (because mixtures of truncated normal distributions will not be normal), but we should be able to calculate the mean and variance for the “next” year exactly.
I actually watched this yesterday. As I understand it, Raw Matt (or Iron Matt as he now prefers to be called) has had a number of run-ins with the truth. He has been called out for academic misconduct of some kind as well, though I don’t know the details.
I saw a video of his recently where someone pointed out that he didn’t know what a p value was. He defended himself by saying “what else could it stand for in the graph other than ‘percentage?’” (or maybe “population,” I can’t remember). Regardless it made me feel a little sorry for him. He doesn’t debate to much anymore. He likes to stick to editing.
I think it might be time for me to reveal my super villian origin story…
Now, I’m going to have to admit something to you that may change your opinion of me. I hope this doesn’t ruin my budding reputation in the community but… (Deep breath) … I’m a lawyer by profession .
Not everyone likes lawyers, but to be clear I’m the kind that likes to fight for the little guy. My focus these days is class actions, like instances where there have been systematic abuses of large numbers of vulnerable people by government institutions. But I used to do quite a lot of cross examinations, and it is one of my favorite parts of the job. I don’t get a chance to do them as often anymore, so getting to scratch that itch is something I enjoy. I also like to think it is something I’m reasonably good at.
I was watching some debates online earlier this summer, and kept seeing instances where people were doing well, but then the YEC guy would slip away. I tried leaving some comments on the videos with suggestions about how those specific aspects of the discussion could be cleaned up, and how the person could have prevented their opponent from slipping away, but found fairly limited reception.
I decided that the problem might be that I had established no credibility in the community in terms of giving advice on how to make the arguments, since I had never taken any of these jokers on myself. Maybe I was falling victim to the Dunning Kruger effect. So I decided to test that hypothesis, and challenged one of the slipperiest fish I thought I could get my hands on–‘Dr.’ Kent Hovind.
From a litigation perspective it went very well. Athiest Junior even agreed and made a video about it. I think the result was, at the very least, entertaining. Here is a link in the event you are curious.
What was important to me in the debate was not so much that I convince Hovind of anything, but that I display my skills in terms of corralling him, controlling the conversation, and getting admissions out of him. The point was (a) to show people that it can be done, and how it is done; (b) to establish some credibility that I know how to do this thing, and that I have something to offer to this community in terms of the technique of how to construct questions and interact with these kinds of people in a live session.
Essentially, my goal was to make the argument that the techniques I employ, and whatever advice I might have about how to employ them, have some relevance and utility to proponents of science should they find themselves in the circumstances of debating with these kinds of people.
Thusfar, my attempt to offer what I consider to be my skills and expertise has gone over like a lead balloon. I have come across as arrogant and presumptuous, and I look like I am “trying to teach my grandmother how to suck eggs.” Worst of all, I have come within a hair’s breadth of offending some of the very people I am trying to impress, and whom I deeply respect.
The reason I’m doing this–the reason it is important to me–is because the anti-science movement in the world today needs to be opposed, if not stopped. Anti-science people are countering scientific arguments with evasive word play and gish gallops. I don’t like that, and I want people to know more about the techniques I use to stop it. I believe I am able to stop it, and I offer the within video as evidence.
That video has found some traction, but I thought perhaps next I ought to tackle someone on more technical topics. Hovind’s only skill is evasion, he doesn’t understand the science whatsoever, and a lot of people won’t even watch him anymore. If I want to show that this sort of technique is useful for science, perhaps I better discuss something that requires a bit more science literacy. So that’s why I am doing this round with Donny. He’s the toughest, highest profile guy I can get my hands on with respect to the subject of genetic entropy (I don’t have Sanford’s phone number).
So, that’s my rant, and the reason why I am wasting my time on these guys. Really, I am not arguing with them. I’m arguing with you.
So I guess that leads to my question: what do you think? Is this worth doing?
You can relax - I think most of us figured that out already.
You think it’s worth doing or you wouldn’t be doing it. That’s OK. Your motivation is not strictly science, but the form of the argument, which is a different perspective than most. That is interesting too.