Evolution vs Creationism

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I see one of two possibilities: (1) You linked to the wrong article, or (2) you're talking as a biologist whereas NOG and Ziad are speaking in layman's terms.

Based on what I know of you guys, I'm going with #2. I understand what NOG and Ziad are trying to express, but they lack the background necessary to do so. Iku is correct in what he says, but I think you may be arguing two different things.

It is a well documented fact (as the study shows) that some genes have much higher mutation rates than others. Therefore, mutations are not completely random. I think the confusion is that Ziad and NOG interpreted you statement of "non-random" to mean directed (or something similar), and that clearly isn't the case either. Mutations are random insofar as genes are not actively working towards a different state. But it is equally true that some genes have far higher mutation rates than others, and thus the chance of any given gene mutating is not random.

(Iku, perhaps you can take a stab at a better explanation as well. Without any background in genetics, I doubt they are going to fully understand that article. - I'm not trying to insult the intelligence here of NOG or Ziad, I'm just suggesting that linking someone to an article like that is not the easiest way to acquire information that you are unfamiliar with.)

 

I don't feel like going into a long-winded explanation, since I have work to do, so I'll keep this short.

The rate of mutation of a gene is one thing, the randomness or non-randomness of mutations in another entirely. Random doesn't mean "all genes mutate at the same rate" (they don't and epigenetics is one of many reasons why). Mutations are random, like it or not. They are described by a probability distribution, and the very DNA change that causes the mutation in the first place is a chance event (this is the key word behind defining them as random). Linking to a paper that is looking at phenotypes (in other words at viable mutations) isn't exactly the best way to disprove this. Of course not all mutations have the same viability; even before getting there the various repair mechanisms have wildly varying efficiencies depending on the specific type of mutation (CpG mutations are notorious for their high frequency and for being extremely inefficient to repair, so naturally a CpG methylation in GC-rich region will frequently form a mutation hotspot). Keep in mind what random means in this context (and in science in general): not "has no pattern", as we tend to use it in everyday talking, but "can be described with a probability distribution" (in other words it HAS a mathematical pattern but which "path" it follows along the pattern isn't predetermined).

Aldeth, I appreciate you not trying to insult my intelligence, but you ended up insulting my career choice instead

I should add this to make it perfectly clear: "random mutations" (almost) never refers to the chances of a particular gene mutating, but to a base change at the DNA level.

 

I'm sorry Ziad.

To paraphrase the cliche, the more one assumes, the more one runs the risk of making an ass of himself.

I knew NOG was an engineer, and as such is a much more math-oriented person. While I was unsure of your profession (this is obvious in hindsight), for some reason I thought you were an engineer as well. As it certainly appears that you are at the very least a biologist, and possibly a geneticist, I humbly apologize for grossly underestimating your knowledge in the field. If you are a geneticist, your knowledge base exceeds my own.

If I may ask, what is your specific area of concentration? As an undergraduate, my concentration was in evolutionary biology, which obviously includes a healthy dose of genetics. At the graduate level, I switched over to biochemistry, and that got even heavier into the genetic side of things, but neither would be as in depth as someone who actually had their concentration in genetics.

 

No need to apologise, I made that comment in jest. The paragraph above it was targeted mainly at Iku.

Technically I'm a molecular microbiologist and not a geneticist. However just about everything I do ends up going back to genetics in some way. There's not much you can in molecular biology without having to poke at genes, sooner or later. I'm currently trying to figure out WHY my mutant makes spaghetti filaments when I don't give it salt (funnily enough it's NOT due to the mutation I introduced in it...) and that's sending me even further along that path.

 

Aldeth, why did you decide to mediate? I was really looking forward to a serious geek throw-down here....

 

Ye gods, I only just noticed how geeky my post is. And I was going for a layman's explanation too...

(OK I wasn't with the CpG example, but that was the only bit I meant to sound scientific)

 

Well, to be more precise, if the point wasn't clear enough already, I wasn't trying to disprove mutations being random. It was the when and where in the sentence of

Gene regulation aside, mutations via transposons or viruses, are genetic mutations and they can cause phenotypic variation, enough so that it has the capability to affect the organisms phenotype, behavior and its reproduction, thus making a new species. What is even more interesting is that they aren't even random in the sense of having no pattern, not completely.

At least two invertebrates already come into mind: Wasps use genes stolen from ancient viruses...

Elysia chlorotica

 

I admit I didn't read all of either of those, but it seems the gist is that some genes are more mutable than others. That's still subject to random chance, though, it's just that the odds aren't even. Think of it like this: if you get a 6-sided die and paint 5 of the sides with a 1, and the other with a 6, you only have a 1/6 chance of getting a 6, while a 5/6 chance of getting a 1. It's still random what you'll roll when, though. Any single roll of the die has a 1/6 chance of getting a 6. It's random, dependant on chance.

Again, I didn't read the entire articles, so please correct me if I jumped to conclusions.

As has been pointed out, I'm an engineer, so I tend to think in math, physics, and system functionality. I'm passingly aware of the basic biochem of genetics and various cellular properties and functions, but not in any detail. That being said, though, mathmatical randomness and biological randomness seem to be the same thing: dependant on chance, usually statistically definable with sufficient study. As with my die example, the odds of each possibility are quite plain and easy to calculate, but that will never tell you what the next die roll will come up with, because the results are random. It seems that the same is true with genetic mutation. You may be able to determine the odds of X part of Y gene mutating in Z manner, but you can't say, "it will happen in 36 hours". You may be able to say, "It's highly likely to happen within 36 hours", but that's not really the same thing. That admitts that it's possible it will happen earlier, or later, or possibly even not at all.

And, as was pointed out above, the processes of selection are far from random, but they are a seperate mechanism from the mutations themselves.

 

@NOG: You might want to check my previous post...I did an update there...

 

Nothing is random in a deterministic universe. As far as I know, this universe is, at least on an atomic level, deterministic.

 

Oh, no, you aren't disagreeing with me. You're disagreeing with a book I read and a documentary I watched.

That said, I should have been more specific in my comments. What the book and documentary both referred to is the fact that cockroaches are far more prevalent right now than they would be if we were gone. They concluded that after nature reasserts itself and cockroaches no longer benefit from a climate controlled environment free of most predatory influences, their populations would be much smaller. In nature, cockroach reproduction ebbs and flows. Indoors, it continues unabated because the climate is always the same. Without humans controlling the environment, cockroaches would reproduce less, and the simulaneous increased predation would make it a double whammy. While their numbers would be substantially reduced, that is mainly because there are more cockroaches around then there should be.

Regarding the "certain regions" where cockroaches might not survive I alluded to, I was referring to what the book and documentary concluded would happen to alien cockroach populations found in regions so cold that cockroaches are incapable of surviving outdoors.

 

There's pretty much nothing deterministic about radioactivity, and electron spin and/or their energy levels is quite a mess as well.

Being able to predict results within extremely low margins of error using statistical methods does not make things deterministic, it just makes the underlying stochastic process well understood AND relatively stable.

 

Iku, those two articles are interesting, but I don't see how they chance anything. In one, a favorable transposition of DNA from virus to host spread through the offspring and eventually the whole group of wasp species. In the other, a creature is capable of absorbing foreign DNA and becoming a plant/animal hybrid (wierd, sci-fi stuff here), but each generation has to do it again and again, which tells me it isn't the kind of mutation we're talking about here, and I'm not sure it counts as a mutation at all. More like a re-fitting or something.

The first is still random and the second, while predictable, is only predictable because random mutations reached a point where this process could (and had to) be redone in every generation.

As for the deterministic universe, Chaos Theory and quantum theory are fun things. Until we understand the latter better, though, we can't really say if the two can mesh or not.

 

At the atomic level, maybe. At the biological level, probably not. At the subatomic level, most definitely not. Schrodinger and Heisenberg showed this rather elegantly (it's called the uncertainty principle for a reason ).

Thanks for clarifying, this makes sense. I hereby revoke my disagreement with you, err, with the book and documentary

 

And this is the point I'm trying to highlight. Up to a point, the when and the where of a gene mutating and that mutation carrying down the germ line is random.

Basic evolution concepts: fidelity, fecundity and longevity. Any piece of replicating material having these properties, getting them through random processes, do so by being able to limit the randomness of the mutations caused by the environment.

You start a game of rolling a die. The rules are simple, you roll the die as long as you get a six. If you get a five or a six it's game over. If you get a one, you get 20 cents. Good?

Now what if, instead of game over with five and six, during the game you'd get to buy yourself the possibility of rolling the die again every time with a 5, but only if you get 4 consecutive rolls of 1 and only if you play an extra fee of 10 cents when you roll the 5, otherwise it's game over again? It's not perfect, there's always a cost, but you get the chance of playing the game longer, thus increasing the chance of making more money.

The game is still a game of chance, I'm not arguing that there'd be a determined result to each roll of the die, but during the game there is a difference with the levels of randomness and the important thing is that the player who doesn't have enough money to make the throw of a 5 better than game over will more likely have less money in the end than a player who is able to make the 5 better and will do so.

Fecundity, fidelity and longevity are evolutionary jackpots. Any replicating entity hitting these will change by chance the probability of getting to play another round. Any replicating entity getting the ability to manipulate the randomness to any extent, improves it's chances of survival in a hostile environment.

 

A few things in that game analogy lost me, but I think I understood what you meant. We're just talking about two different types of randomness by and large. For the last bit, the bit about manipulating the randomness, I'm guessing you're talking about that sea slug and the like. As I understand it, that is rare enough to be discounted, and is not of the nature of an evolutionary mutation, but rather of an evolutionary adaptation as a result of mutation, much like having an opposible thumb is. That this adaptation manifests itself as an intentional, repeated change to the genome is truely bizzare, but not really relevant to the discussion.

Now, a creature like what sometimes pops up in bad sci-fi horror, one that absorbs the DNA and characteristics of it's prey in a manner that is passed on through generations, to the point where it can select characteristics that it likes and keep them while discarding others, and target prey with the intention of gaining their advantages, that would be something else. To my knowledge, though, that doesn't exist.

 

If the universe is deterministic at the atomic level, then it is deterministic at all upper layers. Given that chemical processes and biological entities are subject to nothing other than the laws of physics, this would also mean that biological processes are subject to determinism. The Uncertainty Principle deals with determining both aspects of a particle and says nothing about determinism. The jury is still out on the matter whether the subatomic level is deterministic, since there still are interpretations of quantum mechanics that include hidden variables and are deterministic, such as the Bohm-Interpretation.

If the universe was not deterministic, but probabilistic, then I would like to use the following quote:

but of course: Un bon mot ne prouve rien.

 

There is actually a very serious school of quantum physics that suggests that everything that appears deterministic and bound by physical laws on the larger scale is actually just the product of the law of averages: that on the quantum level everything is random, but things average out into a constant when you amass great numbers of quanta.

 

Mm, nice...

This: gene duplication providing the raw material for generation of morphological diversity

...now this is what I've been looking for...

This interesting notion, that Stress Increases Genetic Diversity is what I've been trying to point out.

And here's one with H. pylori. This should be very interesting read: A paradigm for direct stress-induced mutation in prokaryotes

 

Well, I only read the abstracts of those articles, but it still sounds like they're talking about things that modify chances, not remove them. Stressors make mutation more likely and more frequent, but don't directly cause them or shift them into a finely predictable, deterministic mode, for example. You may have gone from a Roulette table to a game of Craps or Texas Hold'em, but it's still a game of chance.