Evolution question - how does complexity arise?

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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Sat May 04, 2013 7:09 am UTC

Ben, at this point your complaints are so Purple I'm not even sure what Tuesday you're swimming against.

Technical Ben wrote:For example, if talking about SDM, I see that it happens in both the lab and in nature. I see no "trick" there, it's a plain observation. Is a scientist "tricking" people when he applies SDM? No. Is nature "tricking" people? No. However, in nature there will be differences to in the lab. Why? Because we are not replicating the natural system 1) Completely and 2) perfectly.
SDM means 'site directed mutagenesis', and is a technique whereby a scientist generates a point mutation in a plasmid. A mutation, which is what you're maybe thinking of here, is when replication machinery copying the DNA of an organism makes a mistake, and generates a point mutation.

Technical Ben wrote:Why is this important? Random systems look different than systems with mechanisms of action.
Yes, but mutation being a random system that generates random mutations (...) is not the same as a scientist deliberately generating a point mutant via SDM. I.e., one system isn't random, and the other system is. They may have the same outcome (single base pair changes), but that says nothing of their mechanism of action, or 'motive force'.

Technical Ben wrote: I want to know the difference between "a person in a lab making these things" and "nature making these things". Does the scientist select randomly, or for a specific mutation? Does nature select randomly or for specific mutations?
See, this is a principal example of why you're frustrating. If you had just said from the very beginning "I do not understand what SDM is" you could have avoided now three posts that make very little sense.
SDM, as I mentioned and as I think we went over in the other thread, generates a single point mutation THAT THE SCIENTIST CHOOSES. This is different from natures random mutations! This has nothing to do with natural selection, per say, because SDM is a molecular biology technique done in the lab. Please stop confusing the two.

I've repeated myself in this post, because as typified by much of your confusion, I want you to pay attention to the things being said to you in an effort to incorporate it into your own mismashed understanding of biology. Having a contention with a theory because you fear the lab techniques developed to study a facet of the field are indistinguishable from real world observations is... I don't even know how to explain to you how demonstrative it is of an appallingly incomplete understanding of the field itself.
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Re: Evolution question - how does complexity arise?

Postby qetzal » Sat May 04, 2013 2:11 pm UTC

Technical Ben,

Keep in mind that when we say naturally ocurring mutations are "random," we mean their occurrence is not related to their effect. An organism has no way to somehow 'decide' what mutations will happen in order to achieve some particular outcome. This has been explicitly demonstrated in bacteria. It's not practical to test directly in larger organisms, but the pattern of mutations observed in all organisms to date is highly consistent with directionless mutation, not with directed.

In contrast, random mutation does NOT mean all possible mutations are equally likely. We know that's not true. Some classes of mutation are more likely than others, for well understood biochemical reasons. E.g. an A is more likely to mutate to a G than a C. But that's true regardless of whether a G or a C is a 'better' mutation for the organism.

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Re: Evolution question - how does complexity arise?

Postby firechicago » Sat May 04, 2013 2:38 pm UTC

Ben, the way you're using the terms "random" and "selection" makes me think you're still unclear on how selection actually works. Selection is random in the sense that it is not strictly mechanistic (mutations generaly do not guarantee either survival or extinction, merely influence the probability of each), but certainly not random in the sense that all outcomes are equally likely, or that we can make no predictions about it. After many weeks and two threads, I'm not at all sure how to get this across to you. Also, your "I'm just looking for alternative explanations for the evidence" schtick is getting really old. There is one commonly accepted explanation for the origin of the diversity of life on Earth. If you find that explanation unconvincing it is your responsibility either to point out its flaws, or advance an alternative explanation, both of which involve actually educating yourself about evolution and the evidence for it, not merely whining about how you don't understand it and therefore it must not be true.

But to respond to your hypothetical, there's a simple method to establish common ancestry. For any life that looks at all similar to what we observe on earth to propagate itself it needs to do certain basic things, like transcribing proteins from genetic material. In organisms with a common ancestor we would expect the genetic code responsible for these basic functions to be very similar, because there is a high probability that any mutation would disrupt these basic processes and result in non-viable offspring. If there were multiple independent origins of life, we would expect these functions to still be served, but there would be no reason for the underlying genetic code to look similar.

If we want to take this a step further, we could identify homologous structures in the genetic code and examine them for differences which do not affect their function. If we assume that mutations arise randomly at a rate more or less constant across the genome, we can predict that organisms which have a common ancestor ought to have roughly the same rate of these funtionless differences across their genome, representing the expected number of mutations occuring in the generations since the common ancestor. If we find that site A and site B have a statistically significant difference in this mutation rate, then that would be a problem for the hypothesis of common ancestry. If there are no such discrepancies, we can use this mutation rate as a sort of "genetic clock" to figure out how recent the common ancestor of two organisms is, and use that information to produce a family tree based on which organisms are more or less recently related. If this produces a tree which is more or less consistent, that's evidence for common descent, but if there are lots of contradictions then that's evidence against common descent.

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Re: Evolution question - how does complexity arise?

Postby gmalivuk » Sat May 04, 2013 2:46 pm UTC

Technical Ben wrote:So no, I don't want to know the difference between nature and a deity. I want to know the difference between "a person in a lab making these things" and "nature making these things". Does the scientist select randomly, or for a specific mutation? Does nature select randomly or for specific mutations?
You *say* you're talking about a person in a lab, but that person is playing essentially the same role that an intelligent designer (i.e. deity) would, and it's clear from your posts elsewhere that you seem to prefer religion over accepted science, or at the very least you would very much like to place them at the same level. Pardon me for connecting the dots.
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One thing that you still fail to get, despite repeated efforts to explain it to you, is even the most basic explanation of how selection works. For example, however the scientist "selects" mutations, that's presumably done before the mutation occurs, while the natural selection of nature happens after the mutation occurs, and so is based on fitness, which is not random.

And the point which was made before I posted about it and which I have already made once (if I have to make it a third time you'll be done with this thread like you were done with the other) is that any point change the scientist makes *could* in principle also happen through a "random" point mutation, because no point mutation is physically impossible. In the opposite direction, of course the scientist *could* in principle make changes in such a way that they are indistinguishable from natural mutations, because random choices from the same distribution are impossible to tell apart.

firechicago wrote:Selection is random in the sense that it is not strictly mechanistic (mutations generaly do not guarantee either survival or extinction, merely influence the probability of each), but certainly not random in the sense that all outcomes are equally likely, or that we can make no predictions about it.
Right. A lot of people make this mistake, though fortunately most of them stop making it once they've been corrected several times...
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Re: Evolution question - how does complexity arise?

Postby Angua » Sat May 04, 2013 2:57 pm UTC

Technical Ben wrote:Why is this important? Random systems look different than systems with mechanisms of action. I could even look for Gaussian distributions, right? If I was looking at the stars and ask an astronomer "well, the motion of the stars look like they follow some rules, do they?" and the answer was "oh, it's all random motion", I'd be rather concerned about such an astronomer. But yet it's suggested mutations are random. So, I am looking to see where in the system of evolution the "rules" are applied. I can't apply rules to the mutations, yet we can agree there are specific rules in evolution.

This confused me. There are many things that are partially random in nature (I am not a physicist so someone can feel free to correct me if I get stuff wrong) - Brownian motion, radioactive decay (half-life gives probabilities but which individual atom will decay next is random). Mutations are similar - we have the probabilites of how often mutations will occur which is influenced by things like the organism in question (eg viruses have different mutation rates, bacteria have different mutation rates, eukaryotes have different mutation rates), which part of the genome you are looking at, etc, but we will not be able to predict exactly which mutation will occur and when.
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Re: Evolution question - how does complexity arise?

Postby elasto » Sat May 04, 2013 3:04 pm UTC

I must admit, I'm struggling with the title question: How does complexity not arise? Given that mutations happen more or less at random, and some mutations are bound to make an organism more complex (for a given definition of 'complex' - eg. a doubling of the green gene followed by turning it to red), and some such mutations are bound to give an organism a survival advantage, surely it would take outside intervention to prevent life becoming more sophisticated over time?

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Re: Evolution question - how does complexity arise?

Postby firechicago » Sat May 04, 2013 3:16 pm UTC

elasto wrote:I must admit, I'm struggling with the title question: How does complexity not arise? Given that mutations happen more or less at random, and some mutations are bound to make an organism more complex (for a given definition of 'complex' - eg. a doubling of the green gene followed by turning it to red), and some such mutations are bound to give an organism a survival advantage, surely it would take outside intervention to prevent life becoming more sophisticated over time?

I think the question is often prompted by a view of mutation that only includes point mutations, because those are the simplest to understand and model mathematically, and therefore are the ones that show up most often in layman's descriptions of how mutation works. Of course the same characteristics that make them easy to understand and model make them less likely to produce actual adaptive mutations, which leads to a lot of misunderstanding.

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Re: Evolution question - how does complexity arise?

Postby selfassembled » Mon May 06, 2013 7:32 am UTC

I haven't read the thread but I would like to post my thoughts on the subject of emergent complexity. The environment of an organism, consisting of basic physical hurdles such as gravity and the weather, as well as competition with other organisms of same and different species, contains a (very) large number of properties evolutionary development can respond to or manipulate. Although random in origin, the process of natural selection by this environment imbues surviving mutations with information about one or more of these qualities. An mutation which increases the amount of fur on an animal, perhaps by changing the keratin protein or its dosage compensation or any number of methods, when chosen by a cold environment, literally carries information about the temperature of the environment. The information content of a genome expands in this manner and can only shrink when two criteria are met, (1) that the mutation is no longer necessary in the environment (ex. a predator is now extinct) and (2) that the mutation's benefit comes at a cost.

That said, complexity is something I still haven't decided how to quantify. The complexity of an organism may have some relationship to the relative entropy or an organism to its surroundings (I believe humans with their highly active and energy hungry brain are top of the pack in this regard) but at a more elementary level it may have more to do with gene count (also considering the more conformational aspects of DNA). The definition of complexity is critical to the question, and for me determines whether properties of increasing complexity extend beyond the natural selection of single and multi cellular organisms forward into our corporate development of technology and back to the development of stars and planets and even atoms as certain configurations of subatomic particles which most accurately portray the information of the laws of physics at small scales.

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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Mon May 06, 2013 1:09 pm UTC

selfassembled wrote: but at a more elementary level it may have more to do with gene count
Oops. There are many, many organisms that have far more genes than humans. It's a very poor metric; protein coding genes? Individual numbers of proteins possible? 'Stuff doing genes' (good luck measuring that!)?

Parasites go through multiple host organisms; that requires insane complexity! Are parasite's the most complex?
Also;
selfassembled wrote:that the mutation is no longer necessary in the environment (ex. a predator is now extinct) and (2) that the mutation's benefit comes at a cost.
I disagree with these two terms with respect for 'information loss'; genetic information is lost when 1 ) individuals that bear new mutations die, and 2 ) populations become extinct or *3* ) when mutations are not passed on
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Re: Evolution question - how does complexity arise?

Postby elasto » Mon May 06, 2013 1:21 pm UTC

That link contains a couple of paragraphs very pertinent to this thread and worth emphasising:

About 70 million years ago, some lucky mishap in the process of cell division led to a triplication of the Solanum genome. The two spare copies of each gene were free to change through mutation. Many were useless and got dropped from the genome, but others developed useful new functions.

The tomato genome team has been able to visualize the result of this triplication by comparing the tomato’s genome with that of the grapevine, a distant relative from which it parted company about 100 million years ago, well before the triplication event. Some of the grape’s genes have a single counterpart in the tomato genome, some have two counterparts and some have three.

Usually the triplication of a genome would be a considerable handicap, saddling a plant with three times as much DNA as it needs. But this event occurred around the time of the catastrophe in which the dinosaurs perished, and the extra genetic versatility may have been a lifesaver. “It’s easy to think that in that period, with a lot of volcanic activity and little sunlight, the reservoir of a lot of additional genes would be useful to a plant,” said Jim Giovannoni, a plant geneticist at the Boyce Thompson Institute for Plant Research in Ithaca, N.Y., who led the American contribution to the tomato genome report.

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Re: Evolution question - how does complexity arise?

Postby selfassembled » Mon May 06, 2013 3:11 pm UTC

Izawwlgood wrote:Oops. There are many, many organisms that have far more genes than humans. It's a very poor metric; protein coding genes? Individual numbers of proteins possible? 'Stuff doing genes' (good luck measuring that!)?

Parasites go through multiple host organisms; that requires insane complexity! Are parasite's the most complex?
Also;


I was merely trying to mention examples for argument's sake, you're mostly right here.

Izawwlgood wrote:I disagree with these two terms with respect for 'information loss'; genetic information is lost when 1 ) individuals that bear new mutations die, and 2 ) populations become extinct or *3* ) when mutations are not passed on


But, in my understanding at least, mutations, being entirely random in nature, cannot carry information until some transformation has taken place, such as natural selection of few among many random mutations (this addresses 1 and 2). Number 2 does make sense though.

Any points on the broader concepts mentioned?

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Re: Evolution question - how does complexity arise?

Postby doogly » Mon May 06, 2013 3:47 pm UTC

You don't want complexity to be working like entropy or information. Entropy is 0 for the vacuum and maximized for thermal equilibrium (opposite for information), but both of these are in a sense not very complex. Complexity is a weird thing which peaks in sort of the middle. Mostly, I wouldn't worry about it. The only thing that gives people a sense that "complexity arising" is a problem is their own gut. It's not like evolution is violating the second law of thermodynamics or the conservation of energy.
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Re: Evolution question - how does complexity arise?

Postby elasto » Mon May 06, 2013 4:53 pm UTC

Yeah. Complexity is a surprisingly complex concept.

Also, complexity in and of itself is no particular advantage evolution-wise. While the human brain is the most complex organ in the known universe, humans are not really the dominant lifeform on earth. For every human who has ever lived, about 1019 insects have lived. And every human being contains around a quadrillion bacteria, so the number of bacteria currently alive and the number that have ever lived are unimaginably large numbers. Most extinction-level events that would wipe out humanity would be shrugged off by 'lesser' species.

Humans are a weird evolutionary niche - a local maximum in the fitness landscape - but we are nowhere near the overall peak. Once we take full control of our genes and have full mastery of nanotech that will be a game changer, but until then we're just a novelty sideshow really.
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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Mon May 06, 2013 4:56 pm UTC

selfassembled wrote:I was merely trying to mention examples for argument's sake, you're mostly right here.
Right; the point we've been discussing is that 'complexity' is poorly defined. I was underlining that your proffered definition suffers from some issues as well. Care to indicate where I'm incorrect?
selfassembled wrote:But, in my understanding at least, mutations, being entirely random in nature, cannot carry information until some transformation has taken place, such as natural selection of few among many random mutations (this addresses 1 and 2). Number 2 does make sense though.
You'll have to explain what you mean by 'carry information'. Any mutation that occurs in the germ line 'carries information', insofar as it being passed on. Any mutation that changes the amino acid called for 'carries information' insofar as it 'changes something'. What do you mean by 'transformation', because that means something in biology and I don't think it means what you think it means.
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Re: Evolution question - how does complexity arise?

Postby doogly » Mon May 06, 2013 5:00 pm UTC

Eh, my money is still on cockroaches outlasting us, but unfortunately I wouldn't ever get to collect on that.
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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Mon May 06, 2013 5:04 pm UTC

The ability of highly proliferated and heterogenous species to remain in the face of massive global change is impressive and speaks to their adaptability, but it doesn't mean they're the 'top of the dogpile'. I'm impressed with the arthopod bauplan, I mean, Beetles, good job, but I'll take brains over it in the long run.

Brains will get us off planet, will bend the cosmos to our will. Before the Overmind, the Zerg was pretty unimpressive.
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Re: Evolution question - how does complexity arise?

Postby elasto » Mon May 06, 2013 5:17 pm UTC

Izawwlgood wrote:The ability of highly proliferated and heterogenous species to remain in the face of massive global change is impressive and speaks to their adaptability, but it doesn't mean they're the 'top of the dogpile'. I'm impressed with the arthopod bauplan, I mean, Beetles, good job, but I'll take brains over it in the long run.

Brains will get us off planet, will bend the cosmos to our will. Before the Overmind, the Zerg was pretty unimpressive.

I dunno. It's not like other species can't leave the planet as well. Hell, maybe Earth was seeded from elsewhere to begin with. (Unlikely, obviously, but somewhere in the universe it has probably happened.)

Brains will get us off the planet, but only if they don't kill us first. The chance of us creating a genetically engineered virus or nanotech that wipes us all out is probably higher than the chance we successfully transition off-world.

Also:
You'll have to explain what you mean by 'carry information'. Any mutation that occurs in the germ line 'carries information', insofar as it being passed on. Any mutation that changes the amino acid called for 'carries information' insofar as it 'changes something'. What do you mean by 'transformation', because that means something in biology and I don't think it means what you think it means.

By information I assume they mean something that holds meaning. It's another surprisingly tricky concept to nail down. If I flip a coin a thousand times and tell you the results, that's a whole lot of data but not a lot of information. Probably the only thing you'll conclude from that is whether my coin is fair or not.

Individual mutations likewise represent lots of data but not much information. Mutations that survive the selection process do start to carry information though: information about the selection pressures those individuals were under at the time (eg. weather, gravity and such, as they said)

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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Mon May 06, 2013 5:27 pm UTC

elasto wrote:I dunno. It's not like other species can't leave the planet as well.
Presumably by developing brains...

elasto wrote:The chance of us creating a genetically engineered virus or nanotech that wipes us all out is probably higher than the chance we successfully transition off-world.
Ehhh, I disagree, but ok.

elasto wrote:By information I assume they mean something that holds meaning...Individual mutations likewise represent lots of data but not much information. Mutations that survive the selection process do start to carry information though: information about the selection pressures those individuals were under at the time (eg. weather, gravity and such, as they said)

All mutations 'carry information'; they're changing the information that's there. Even mutations that don't change what amino acid is called for 'carry information', as a subsequent mutation to that triplicate may no longer result in a redunant change. And, again, 'surviving the selection process' says absolutely nothing about the conditions the organism is under. It just tells you that the mutation didn't kill the organism. Unless you have the ability to look at a string of basepairs and say "Oh ok, I see that cytosine has changed to a thymine, that must mean the organism lives in a highly saline environment!", which would be pretty damned remarkable.
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Re: Evolution question - how does complexity arise?

Postby doogly » Mon May 06, 2013 5:31 pm UTC

A shell game with "information" and "meaning" is pretty obviously useless.
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Re: Evolution question - how does complexity arise?

Postby elasto » Mon May 06, 2013 5:36 pm UTC

Izawwlgood wrote:
elasto wrote:I dunno. It's not like other species can't leave the planet as well.
Presumably by developing brains...

No, by being carried off as spores.

All mutations 'carry information'; they're changing the information that's there.

That's not a change in information, that's a change in data. The reason a brain is the most complex organ in the universe is because of the information embedded in its structure. It would take as much data to perfectly clone a 3 pound lump of rock as it would a 3 pound brain, but the arrangement of the neurons in a brain holds much more significance than the arrangement of particles in a rock.

Yes, the concept of information is a very subjective one. If I give you an encrypted file, it's just random noise to you; But to someone with the key that noise suddenly becomes information.

Mutations are just random noise. Mutations plus selection are useful information from which knowledge can be inferred.

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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Mon May 06, 2013 5:45 pm UTC

elasto wrote:No, by being carried off as spores.
Oh, certainly, and panspermia is pretty cool. Not quite the same thing, not really on any sort of biologically useful timescale, and only applicable to a limited subset of life. But yeah, certainly.
elasto wrote:Mutations are just random noise. Mutations plus selection is useful information from which knowledge can be inferred.
Your statement was;
elasto wrote:Mutations that survive the selection process do start to carry information though: information about the selection pressures those individuals were under at the time (eg. weather, gravity and such, as they said)
And at the risk of getting even more sidetracked than we already are, I'm trying to tell you that you seem to be lumping 'mutations' and 'phenotype' together as the same thing. Mutations are just changes to DNA; you cannot infer anything about the environment based on looking at mutations alone. You're jumping up a few levels of organization here.

Given how confused one poster already got confused as to what mutations are, I'm still waiting to hear what selfassembled meant so we can clarify.
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Re: Evolution question - how does complexity arise?

Postby Technical Ben » Mon May 06, 2013 6:06 pm UTC

lzawwlgood. Thanks for the reply, sorry if I confused terms or subjects there. Does SMD differ from "a point mutation" through replication errors? Are replication errors the only method of mutation, the most common, or just one method? If the two observations are the same, then I can be happy the observed results in the lab are what I'm being suggested happens in nature. As we cannot observe every mutation in nature, and the argument is "by the numbers there must be the mutation we want out there at some point in history". The "some point in history" bit is what I cannot observe, so I need to look at indirect proof (as we do with particle physics or astrophysics). Thanks.
Yes, but mutation being a random system that generates random mutations (...) is not the same as a scientist deliberately generating a point mutant via SDM. I.e., one system isn't random

Ok, if the scientist acts randomly, are his results the same as in nature? This is something I can look at. If I look at the figures, do I find the same results of mutation sites made at random in the lab and the resulting phenotype as I see outside the lab?

Sorry for not understanding that SMD was a specific site mutation in this instance, I thought in your reply we were already assuming the scientist was acting randomly like nature does. Less an error in what the mechanism of SMD is, and what the goal of the lab tests are. I was not arguing for SMD, I just asked how a scientist can cause mutations in a lab, there are non SMD options (radiation/chemicals AFAIK). Would it be better to use these examples as unlike SMD they are similar to the natural system we wish to model. Is this contesting, or just asking for clarity on the description of the systems?

Thanks qetzal, that's a new insight to me. Very interesting. So, would it be a Gaussian curve of the probability of possible mutations? What does it tell us when we see a system with such "rolls" of a dice? Is it a "fair" dice or coin if we do not get an even distribution? Does science not say that there is a mechanism involved then? A trend? I would say a dice that rolls more of some sides than others would be "weighted", it would have in part a non-random mechanism. We could specify an additional property of the dice.

This should be noted, right? We don't call the periodic table "random", do we? So, no, I'm not trying to cause trouble in a forum where I see most follow evolution. I'm asking, why they are we not applying mechanisms to the theory, when there seems to be some?

gmalivuk wrote:For example, however the scientist "selects" mutations, that's presumably done before the mutation occurs, while the natural selection of nature happens after the mutation occurs, and so is based on fitness, which is not random.

Thanks, it seems the assumption was I was asking for a pre-selecting scientist. I was commenting on random selections in the lab and in nature. If I can see how they work in the lab, I can apply them to nature and see if the lab results match the ones in nature. I can confirm the labs actions are "random" through a confirmed random selection method. Then from there see if we get the same trends/matches in nature. I want to check a data set of noise, to see if there is any signal, or visa versa.
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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Mon May 06, 2013 6:36 pm UTC

Technical Ben wrote:Does SMD differ from "a point mutation" through replication errors?
No; *SDM* stands for 'Site Directed Mutagenesis'. It refers to a molecular biology technique wherein a single point mutation is made specifically where you want. So, like I said, you can change ATCGGGCTA to ATCGAGCTA.
In terms of output, this is the same as a point mutation in nature due to, say, a replication error. It is not the same as a replication error, because it is not random.
EDIT: I also want to mention that this is the second time this page I've answered this exact question for you Ben.
Technical Ben wrote:Are replication errors the only method of mutation, the most common, or just one method?
No there are others. ImagingGeek showed you the math on mutation frequencies in the other thread. Deletions and duplications are possible, but probably more drastic. Point mutations have the benefit of at least possibly generating just a change to a protein, instead of abolishing it entirely.
Technical Ben wrote:If the two observations are the same, then I can be happy the observed results in the lab are what I'm being suggested happens in nature.
What 'two observations'?
Technical Ben wrote:If I look at the figures, do I find the same results of mutation sites made at random in the lab and the resulting phenotype as I see outside the lab?
I still don't understand what you mean by this; are you asking if you could wave a wand and randomly mutate one base pair in a plasmid, and compared it to a plasmid that has randomly accumulated a replication error in a bacterium, if you could tell the two apart? I and others already answered that question. If you're asking 'Could a point mutation caused by exposure to a mutagen be differentiated from a point mutation caused by a random replication error' the answer is, again and still, no.
Technical Ben wrote:I'm asking, why they are we not applying mechanisms to the theory, when there seems to be some?
What mechanisms do you think we're not applying to the theory? We've been explaining the mechanisms to you for quite some time now.
Last edited by Izawwlgood on Tue May 07, 2013 1:07 pm UTC, edited 1 time in total.
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Re: Evolution question - how does complexity arise?

Postby qetzal » Mon May 06, 2013 8:34 pm UTC

Technical Ben wrote:Thanks qetzal, that's a new insight to me. Very interesting. So, would it be a Gaussian curve of the probability of possible mutations? What does it tell us when we see a system with such "rolls" of a dice? Is it a "fair" dice or coin if we do not get an even distribution? Does science not say that there is a mechanism involved then? A trend? I would say a dice that rolls more of some sides than others would be "weighted", it would have in part a non-random mechanism. We could specify an additional property of the dice.


Again, the point is that "random mutation" does not mean "all possible mutations are equally likely." It means "the likelihood of a given mutation does not depend on the effect (phenotype) of that mutation." And yes, science does say there are mechanisms that cause some types of mutations to be more common than others. That doesn't make mutations non-random, it just means that they're not evenly distributed.

You'd agree that rolling a single unbiased die gives a random result, right? So rolling two unbiased dice at the same time should also be random, right? Yet if you add the values of two dice, you're much more likely to get a value of 7 than a value of 2, right? That's an example of how events can be random without be equally likely.

With some trepidation, let me extend your dice analogy another step. Let's say that mutations are somewhat like rolling a loaded die. Not all numbers will come up with equal frequency. Now imagine you're playing Monopoly, but you're rolling a single weighted die (instead of two normal dice). The die might be weighted so that the number 5 comes up more often than expected. But that's true regardless of whether a 5 makes you land on your opponents Boardwalk with a hotel, bankrupting you out of the game, or gets you past his hotel to Go, earning you $200. The weighting of the die doesn't change based on the outcome of each possible roll.

Mutations are similar. Some kinds are more likely that others, but the evidence indicates that the chance of a given mutation does NOT depend on whether the effect of the mutation will be good, bad, or neutral. Put another way, direct and indirect evidence indicates that there is no force, internal or external, that somehow causes 'good' mutations to occur.

Technical Ben wrote:This should be noted, right? We don't call the periodic table "random", do we? So, no, I'm not trying to cause trouble in a forum where I see most follow evolution. I'm asking, why they are we not applying mechanisms to the theory, when there seems to be some?


We do apply mechanisms to the theory of evolution. It's just that the evidence says that the frequency of a mutation is not dependent on the resulting phenotype. Thus, we don't apply that particular mechanism to evolution.

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Re: Evolution question - how does complexity arise?

Postby gmalivuk » Tue May 07, 2013 3:26 am UTC

Technical Ben wrote:Thanks qetzal, that's a new insight to me. Very interesting. So, would it be a Gaussian curve of the probability of possible mutations? What does it tell us when we see a system with such "rolls" of a dice? Is it a "fair" dice or coin if we do not get an even distribution? Does science not say that there is a mechanism involved then? A trend? I would say a dice that rolls more of some sides than others would be "weighted", it would have in part a non-random mechanism. We could specify an additional property of the dice.
You need to read up on probability distributions.

Despite attempts (once again, repeated attempts) to explain this to you, you still seem to be under the impression that "random" implies either Gaussian or uniform (despite the fact that those are two very different distributions with lots of possibilities in between, in addition to all the distributions that look nothing like either one).

A weighted coin that comes up heads 90% of the time and tails the other 10% is still random, even though it's obviously not "fair" (where "fair" only means "uniform" because we've decided that's what we want from a coin). Just as a perfectly fair/uniform 10-sided die continues to be random even if you're only concerned with whether the result is 1 (10%) or not-1 (90%), giving the same distribution as the coin.

Similarly, mutations that are more likely to change G to C than to A or T are still random, despite not being uniform. (And yes, there's an underlying mechanism to explain this, but it's purely chemical in nature, and has nothing whatsoever to do with the eventual phenotypic results of the mutation.)
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Re: Evolution question - how does complexity arise?

Postby Technical Ben » Tue May 07, 2013 4:14 pm UTC

Thanks Izawwlgood, I see no where in the description of SMD that requires non-random selection of the site to carry out the procedure. Does it? Am I missing something here?
What 'two observations'?

The lab and in nature. I can't observe every mutation in nature, nor every variable. But we can look at these things in a lab, check controls, check the variables and see which more closely match nature. As you said different types of mechanisms of mutation can give different distributions of results. So do replication errors give a different result than mutations from chemical damage? While both still allow any type of mutation, do they offer the same distribution of mutations?
If you're asking 'Could a point mutation caused by exposure to a mutagen be differentiated from a point mutation caused by a random replication error' the answer is, again and still, no.

Ok, thanks, so from here I would ask, if the two are the same (when applying a SMD at a random site), what do we see in the lab? Can I look at any examples of high rates of random mutations in a lab, and what the results were? I would find the answer "the same as in nature" less helpful than the answer "these are the lab results, lets see if they match nature". One is teaching parrot fashion, and the student learns only how to repeat, the other lets the student learn how to progress.
What mechanisms do you think we're not applying to the theory? We've been explaining the mechanisms to you for quite some time now.

The distribution of the results. As qetzal says, the die may be weighted. I've not argued future phenotypes cause past mutations, have I? Anywhere? But I have asked in past threads if the "mutations" are rolling a fair dice or not. Only now we agree there are weightings. While these do not prevent any specific result, they do tell us the likelihood of finding a specific result. If we are hesitant to admit those observations, are we still playing true to science?

qetzal wrote:Let's say that mutations are somewhat like rolling a loaded die. Not all numbers will come up with equal frequency.

A loaded die has a specific property though. It is weighted or shaped so as to give a certain distribution. To pretend it's "random" is to play false to science, maths and honesty in statement IMO. Else why do we have the "periodic table" and "laws of physics" instead of "random table" and "random laws of physics"? We know both of those have random inputs, but their construction is anything but. We put emphasis on the probability of a result over the possibility of it. Here I see people only claiming it's possible, but making little mention of what is probable. That's fine, but it is why even to gmalivuk's annoyance of "repeated attempts", I still ask not for what is possible but what we observe to be probable.

Gmalivuk, sorry if I came across as if insisting there are only 2 distributions of probability of mutations here. So tell me what distributions we get. I'd not accept someone saying "the periodic table is made by random iterations of matter", it's made by specific iterations that follow laws. Right? Even the distribution of the universe is studied this way, despite it's "random" nature. I know these distributions are random, I know a mutation site is. It's the way the answers are given that speaks louder than what the answers are. For example, if you ask a layman to play a game with a "weighted" dice, would they call the result "fair" or "random"? Or would they give importance to the weighting and the result such weighting favored (if any)?

As to "and has nothing whatsoever to do with the eventual phenotypic results of the mutation", I don't think I ever suggested it does. Unless I ever suggested the first roll of a dice decides what the next roll will be. I'm happy to leave things here, I think the comments on the mutations meet the questions I had. I observed the mutations and/or phenotypes were not "fair/uniform". Either my observations were wrong, or there was some mechanisms involved in this. That's cleared things up now, thanks. :)
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Re: Evolution question - how does complexity arise?

Postby doogly » Tue May 07, 2013 4:20 pm UTC

So, to be clear on what answers would be like for you, you'd like to hear something like "A transcription error that inserts an extra A into an otherwise unchanged sequence is 2500x more likely than a cosmic ray coming in and doing something wacky." But with the full list of what sorts of things happen, and what kind of chemistry gives each one?
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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Tue May 07, 2013 4:24 pm UTC

Ben, this is the second time I've corrected your 'SMD'. It is SDM. This is now the third time I've explained to you what it is, ON THIS VERY PAGE.
Technical Ben wrote:I see no where in the description of SMD that requires non-random selection of the site to carry out the procedure. Does it? Am I missing something here?
*SITE DIRECTED MUTAGENESIS*. It is mutagenizing (changing a basepair to something else) a specific site. It is NOT random, the procedure itself REQUIRES that the scientist CHOOSE what basepair is changed.
Technical Ben wrote:As you said different types of mechanisms of mutation can give different distributions of results. So do replication errors give a different result than mutations from chemical damage? While both still allow any type of mutation, do they offer the same distribution of mutations?
I said no such thing. I said you cannot tell the difference between a single mutation if it is caused by replication error or by chemical mutagenesis or SDM. Mind you! Those are three different MECHANISMS to produce mutations, and they are NOT equivalent in their action, but they ARE equivalent in their outcome.
Technical Ben wrote:(when applying a SMD at a random site)
By 'random site' you can only mean 'I looked at a bunch of DNA, and pointed randomly to a position and said "Oh ok, that's a C, I'm going to change it to, lets say, a G." As in, you randomly SELECTED something, but then DELIBERATELY designed an SDM to mutate it. Do you understand?
Technical Ben wrote:Can I look at any examples of high rates of random mutations in a lab, and what the results were? I would find the answer "the same as in nature" less helpful than the answer "these are the lab results, lets see if they match nature". One is teaching parrot fashion, and the student learns only how to repeat, the other lets the student learn how to progress.
I don't understand what you're asking here, and I don't understand what 'teaching parrot fashion' has to do with this.
Technical Ben wrote:The distribution of the results. As qetzal says, the die may be weighted. I've not argued future phenotypes cause past mutations, have I? Anywhere? But I have asked in past threads if the "mutations" are rolling a fair dice or not. Only now we agree there are weightings. While these do not prevent any specific result, they do tell us the likelihood of finding a specific result. If we are hesitant to admit those observations, are we still playing true to science?
Your problem is you don't understand what mutations are, and you're trying to incorrectly argue why distributions of mutations don't match your understanding, and you aren't listening to the explanations given. So, lets give a very rough overview;
Organisms have DNA. DNA codes for protein. Occasionally, the organism may fail to replicate that DNA exactly, which will cause a very slight change to the proteins the DNA codes for. This is a mutation. This mutation may change the way the protein behaves. It is then selected for or against. Assuming it is passed on, and if selected for, the mutation proliferates in subsequent generations. If selected against, the mutation does not.
Now, how does that disagree with your understanding?
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Re: Evolution question - how does complexity arise?

Postby Sizik » Tue May 07, 2013 4:55 pm UTC

Technical Ben, I think you need to start making a distinction between "random" and "arbitrary". Random means unpredictable or lack of a pattern. If you roll a die, the result is random. Even if the die is weighted to roll a 6 90% of the time, it's still random, even though most of the results will be a 6. Arbitrary means without reason. If you were to pick up a die and put it back down, the face it lands on is arbitrary. You could roll it, producing a random result, or you could choose a side. Either way, it doesn't matter; one of the sides will be facing up and the rest won't.

Often, people use "random" when they mean "arbitrary". A naturally-occurring point mutation is random. SDM is arbitrary; it doesn't matter which base-pair is chosen to be mutated, only that a specific one is. The laws of physics aren't random, in fact they're quite the opposite. They are, however, arbitrary, since they depend on constants whose values are independent of anything else, and there's no reason why they couldn't have radically different values (other than the fact that they might not produce a universe where intelligent life could evolve to observe them).
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Re: Evolution question - how does complexity arise?

Postby D.B. » Tue May 07, 2013 5:02 pm UTC

...A loaded die has a specific property though. It is weighted or shaped so as to give a certain distribution. To pretend it's "random" is to play false to science, maths and honesty in statement IMO...

No, it's just a language issue. Looking on the wikipedia page for 'randomness' the first entry is "...Having no definite aim or purpose; not sent or guided in a particular direction..." which seems to fit your definition quite well.

However, it continues a paragraph later with "...Applied usage in science, mathematics and statistics recognizes a lack of predictability when referring to randomness, but admits regularities in the occurrences of events whose outcomes are not certain..." which is the definition that's being used here.

No one's being "hesitant to admit ... observations". It's just different terminology. And it's probably terminology that you'll have to get used to using, as almost any discussion of scientific matters anywhere will use it.

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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Tue May 07, 2013 5:06 pm UTC

Sizik wrote: SDM is arbitrary; it doesn't matter which base-pair is chosen to be mutated, only that a specific one is.
Well, no; SDM is deliberately choosing a basepair to change, because the resultant change will have use to the researcher. For example, you can replace a serine or threonine with an alanine, and now the protein cannot be phosphorylated at that site. You can replace a serine or threonine with an aspartic acid, and now the protein always behaves as though that site is phosphorylated.
EDIT: What I mean to say, is that SDM is not used as a random mutagenizer.
But yes, for the purposes of our discussion, the product of an SDM that is arbitrarily chosen is indistinguishable from a replication error; everything else you said is correct.
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Re: Evolution question - how does complexity arise?

Postby qetzal » Tue May 07, 2013 6:02 pm UTC

Technical Ben:

Let me ask you this again, since you didn't respond previously. If I roll two standard, unweighted dice and add their values together, is the result random (as you are using the term), or not?

In any case, here's the important issue. We've answered your question, agreeing that certain kinds of mutations are more likely to occur than others. You've agreed that just because mutations are not equally likely (not 'random' as you're using the term), that doesn't mean that "future phenotypes cause past mutations." So what's your point in all this??? What do you think this has to do with evolution or how it generates complexity? Why, in a thread about evolution, do you want to compare naturally occurring mutations to mutations generated in a lab by a human scientist? We know that humans aren't responsible for naturally occurring mutations, and we know that the methods used by humans to generate mutations are not the same as the mechanisms responsible for natural mutation. You deny that your hypothetical human scientist is meant to be a stand-in for some god or intelligent designer, so how is any of this even slightly relevant to evolution?

Maybe you have a real point here, and I'm just not seeing it. Clearly others are having the same problem. So please explain what you're trying to get at so we can have a useful discussion.

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Re: Evolution question - how does complexity arise?

Postby JudeMorrigan » Tue May 07, 2013 6:48 pm UTC

Izawwlgood wrote:
Sizik wrote: SDM is arbitrary; it doesn't matter which base-pair is chosen to be mutated, only that a specific one is.
Well, no; SDM is deliberately choosing a basepair to change, because the resultant change will have use to the researcher. For example, you can replace a serine or threonine with an alanine, and now the protein cannot be phosphorylated at that site. You can replace a serine or threonine with an aspartic acid, and now the protein always behaves as though that site is phosphorylated.
EDIT: What I mean to say, is that SDM is not used as a random mutagenizer.
But yes, for the purposes of our discussion, the product of an SDM that is arbitrarily chosen is indistinguishable from a replication error; everything else you said is correct.

I think you and Sizik are actually saying the exact same thing. That is, I think that Sizik was trying to distinguish between "arbitary" and "random", and that their point was that the process in question was NOT random, even if the scientist could select their desired specific base-pair arbitrarily.

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Re: Evolution question - how does complexity arise?

Postby amylizzle » Tue May 07, 2013 6:52 pm UTC

I realise the topic has shifted somewhat, but I'm surprised nobody has mentioned one of the most important steps in evolution and its increase in complexity, which is the incorporation of mitochondria into early bacteria. The joining together of multiple simple systems is one of the most significant contributors to complexity.

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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Tue May 07, 2013 7:03 pm UTC

JudeMorrigan wrote:I think you and Sizik are actually saying the exact same thing
I think we are too; I just wanted to clarify that SDM is not an experimental method that is used arbitrarily, to, say, produce 'arbitrary' mutations to a protein.
amylizzle wrote:which is the incorporation of mitochondria into early bacteria.
Yeah, endosymbionts certainly allowed for some important things to happen, but aren't really an example of how complexity arises from mutations in DNA. It is certainly an enormously important event in the scheme of life though, that allowed an enormous amount life to actually exist.
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Re: Evolution question - how does complexity arise?

Postby LaserGuy » Tue May 07, 2013 7:27 pm UTC

Agrajag619 wrote:Thank you all again for your responses! ahammel's example here is a solid counter to my arguments - complexity seems intuitively to increase here, however it is defined. This is a serious objection to my views, and indicates that they are flawed in some way, possibly even fatally so. Everyone else, too, has brought up excellent points.

If I cannot find answers to these objections, then of course I will accept evolution. I hope you will understand, however, if I delay a little bit - I'm not ready to make such an important judgment solely on the basis of a brief internet conversation, so I am going to respectfully withdraw from this discussion in order to do further research. I'll make another post here in one year, hopefully with some conclusions. Thank you.


Can we just go back to this and pretend that the rest of this thread never happened? :wink:

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Re: Evolution question - how does complexity arise?

Postby Technical Ben » Tue May 07, 2013 9:08 pm UTC

doogly wrote:So, to be clear on what answers would be like for you, you'd like to hear something like "A transcription error that inserts an extra A into an otherwise unchanged sequence is 2500x more likely than a cosmic ray coming in and doing something wacky." But with the full list of what sorts of things happen, and what kind of chemistry gives each one?

No, I'd prefer an answer that says "the observation of a certain distribution of phenotypes matches the observation of a certain distribution of mutations." Because I only stated I observe specific phenotypes, and the previous answer was lacking with "it's just random", I had no indication if I should be applying a fair/uniform distribution or not. There even seemed to be an insistence that is was uniform distribution. Sorry if that was not the meaning of the posts, it may be we both read each others incorrectly. All I was looking for was a way to match the observations of one thing to the other, or the theory to the observations. I think that's done now. I'll read through others comments, but I do not have anything more to ask for if we are now both looking at the same observations. :)

PS, Izawwlgood, if a scientist cannot roll a die (or RND generator) prior to SDM (yes, it was my dyslexia there that caused a error in letter order previous, sorry) so as to choose a site at random, then I am lost for words.
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Re: Evolution question - how does complexity arise?

Postby dudiobugtron » Tue May 07, 2013 9:24 pm UTC

Agrajag619 wrote:
ahammel wrote: The GoF mutation(s) that resulted in citric acid metabolism in the E. coli long-term experimental evolution experiment is a particularly famous example.


Thank you all again for your responses! ahammel's example here is a solid counter to my arguments - complexity seems intuitively to increase here, however it is defined. This is a serious objection to my views, and indicates that they are flawed in some way, possibly even fatally so. Everyone else, too, has brought up excellent points.

If I cannot find answers to these objections, then of course I will accept evolution. I hope you will understand, however, if I delay a little bit - I'm not ready to make such an important judgment solely on the basis of a brief internet conversation, so I am going to respectfully withdraw from this discussion in order to do further research. I'll make another post here in one year, hopefully with some conclusions. Thank you.


I'm interested in how your belief system works (I understand you won't respond, but I'd like to record my interest anyway!).

It seems like you originally thought that Evolution seemed to explain everything really well, except that it was impossible - and therefore that creation must be the correct theory. Then, you found out that actually evolution isn't impossible. And, if you are able to confirm this in your research, you will then decide that evolution is the correct theory, and therefore creation isn't.

Is that close to being a correct analysis?
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Re: Evolution question - how does complexity arise?

Postby Izawwlgood » Tue May 07, 2013 9:26 pm UTC

Technical Ben wrote:PS, Izawwlgood, if a scientist cannot roll a die (or RND generator) prior to SDM (yes, it was my dyslexia there that caused a error in letter order previous, sorry) so as to choose a site at random, then I am lost for words.
I am beyond uncertain how you can possibly be confused at this point. Putting aside the dyslexic confusion of SDM <-> SMD, which is a completely honest mistake, I truthfully don't understand what you are having trouble with in terms of what site directed mutagenesis is, and it's frustrating, because it makes me think that each explanation I've given you is insufficient at conveying what the technique does.

A scientist CAN roll a die and randomly pick a basepair to mutate (I and others said as much!), but that doesn't mean that SDM is a process used to randomly generate mutations. As mentioned, if you roll a 1d10 and come up with a 4, that's random. If you pick up a 1d10 and place it with the 4 position up, that's not random, and the fact that a die that's been thrown and landed on a 4 is indistinguishable from a die that was placed with the 4 position up doesn't mean the two methods for producing a 4 are identical/interchangable/indicative of whatever it is you keep trying to circle around. Arbitrary vs random vs directed.

And again, I, and I'm not sure anyone really, knows what you mean when you say stuff like this;
Technical Ben wrote:All I was looking for was a way to match the observations of one thing to the other, or the theory to the observations.
Everything matches, everything lines up, and everything fits. Your lack of understanding, the holes in your knowledge, are where your self-proclaimed inconsistencies lie.
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Re: Evolution question - how does complexity arise?

Postby vbkid » Tue May 07, 2013 9:44 pm UTC

Technical Ben wrote:No, I'd prefer an answer that says "the observation of a certain distribution of phenotypes matches the observation of a certain distribution of mutations." Because I only stated I observe specific phenotypes, and the previous answer was lacking with "it's just random", I had no indication if I should be applying a fair/uniform distribution or not. There even seemed to be an insistence that is was uniform distribution.


Ben,
As has been pointed out already, while mutations are random, phenotypes are not directly correlated to the chance of a specific mutation since, as been pointed out already, beneficial mutations are passed on with a much higher rate of success.
Despite my own intuition, I'll even humor you with a dice analogy.
Say there is a child with a lot of loaded dice that comes up "1" 90% of the time and "6" 10% of the time. Now this kid REALLY likes the number 6, so he tends to not disturb those while rerolling any dice that come up "1". An observer could easily see that while "1" has a much higher probability of happening, it doesn't stick around long so only"6's" tend to get passed along. Pretty soon, all the kids dice are "6's".


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