In What Way are Mutations Random

Faith & Science Conversation
41

The difference is in the specifics, IMHO. As I stated in the opening post, an example of a non-random mutation is a specific change at a specific locus in response to a specific environmental challenge. For example, if a bacteria mutated a specific base in a specific base which confers antibiotic resistance, and it does so when exposed to antibiotics. Non-random mutations would be a direct mechanistic connection between the environment and mutations.

Obviously, this is not what we see with DNA repair mechanism and codon optimization. These are very, very general mechanisms that can reduce the overall rate of deleterious mutations (and possibly beneficial ones) while being blind to the needs of the organism (from a scientific point of view).

42

This appears to me to be neutral drift, nutation/variation has been selected on by natural selection, but needs to be cleaned up and organized by the genetic apparatus of the body.

This makes sense according to my understanding of evolution as a process that involves both Variation and Natural Selection. Drift is both. It is genetic change, but it is results in no new change. It is selection in that it improves the was the genes work even though it does not again make any real change, just refinement.

Now please respond. Variation is random to the 3nvironment. Natural Selection is not random, is directly relation to the environment. That makes evolution as a process not random, but relation to the environment.

43

I don’t even know what that means…

I don’t buy into the delusion that anything can be derived from logic. Logic only gives you conclusions based on the premises you choose to accept. It is the basic methodology of rhetoric, whereby you can justify anything with carefully chosen premises. What is true is that logical coherence is the basic requirement something to be meaningful. But the burden of proof here is someone to demonstrate the logical inconsistency in what someone says. Most of the time, especially stated as you have done (as if unaware that what logic gives depends on premises accepted), such accusation just means an inconsistency with the premises you have accepted as true which nobody else is required to accept.

…not much of an insult there…
Aesthetics is a far better basis for conclusions than a delusion of propping up something by logic.

But the truth is that what I have been saying is all about logical coherence. You have to recognize that God’s omnipotence cannot be an ability to do whatever you say by whatever means you dictate because it is trivial to demonstrate that this produces logically incoherent claims.

44

@mitchellmckain

When I started to actually parse Paul’s logic in some of his pronouncements I suddenly realized that he was using RHETORICAL FLUORISHES when he didn’t have the logic to support his position.

If Paul had any idea of original sin (according to Augustine) it was based on some kind of magical or metaphysical state that God invoked… not something that had to do with actual paternity.

And the same goes for Paul’s views on circumcision being prohibited. It wasn’t logic… it was rhetoric.

But Mitchell, I don’t think anyone said that Trinitarian Christianity was SUPPOSED to be logical.

And in the final analysis, back to our original point of contention … if God has the standards set for how to make Adam and Eve into miraculously created humans … then he certainly has the ability to make humans more slowly … by means of God’s chosen design for mutations… invoked for eons until humanity has arrived at the form his plan requires.

45

You are not making any sense. Rhetoric IS logic. Using rhetoric is therefore supporting your position with logic. The problem is that logic can support anything. It all depends on what premises your arguments start with.

Nonsense. The false premise here is that genetics is the only inheritance we have. And the implications of this presumption is abominable which is why you end up with things sounding like a gospel of salvation by eugenics. The more important inheritance are those of ideas – a memetic inheritance – upon which our humanity and the human mind is based. And that is something we have from God before it was corrupted with self-destructive habits starting with A&E. There is nothing magical about this.

Of course they do. Lots of people including me not only say that but require it – for that is the only way it can even be meaningful rather than incoherent babbling. What is incorrect is to say that anything can be derived from logic alone. Trinitarian Christianity is derived from logic and scripture.

God has the knowledge and ability to use the method required for the results He desires.

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@mitchellmckain

Speech-making CAN use logic. But what if you are arguing something that is not actually true?

Then you have to make RHETORIC do the heavy lifting of logic.

For example: Think of how many elections might have been won in the rural political races because one candidate stood up, and with every ounce of outrage he could muster, he said that he was
SHOCKED to find out that his scandalous rival actually MATRICULATED with women while attending
college!

SHOCKING! I say again, SHOCKING!

47

That doesn’t make the arguments any less logical. That is the whole point. Logic doesn’t guarantee truth because the premises with which it starts might not be true. Logic can only take you from premises to conclusions. It can only guarantee the conclusions are true if the premises are true.

Not only that, but the premises can be false even when the conclusion is true. That is one of the dangers of arguments for the existence of God… you can end up replacing your faith in God with faith in a premise which is actually not true.

I am not following your example. Are you implying that the people in rural areas don’t know the meaning of “matriculated?”

48

@mitchellmckain

I chose my words poorly. Let me try again:

“What if one was arguing something that could only be made true by being illogical?”

You DO love to argue, don’t you?

49

Neutral drift can result in phenotypic change, just not beneficial or deleterious change. The example I have often heard is alleles that change the shape of our nose. Not all of those shapes are beneficial or detrimental.

I think the best way to describe evolution is as a stochastic process. Natural selection loads the die for or against certain traits, if you will.

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50

@T_aquaticus, this abatement is not weapons’ to the question I asked. Neutral drift is not a new phenomenon so it would seem that science should have some sort of idea shat causes it, If not please just say so.

stochastic

[stəˈkastik]

ADJECTIVE

technical

  1. randomly determined; having a random probability distribution or pattern that may be analyzed statistically but may not be predicted precisely.

I asked you if natural selection id rendom in connection with wcology and you respond that it is stachastic, which means that it is random, so you are saying that ce3lection is in no way related to the ecology, even though I suspocet that you know that that is noytm true. What the hell is going on?

Natural selection acts on the phenotype, the characteristics of the organism which actually interact with the environment, but the genetic (heritable) basis of any phenotype that gives that phenotype a reproductive advantage may become more common in a population. Over time, this process can result in populations that specialise for particular ecological niches (microevolution) and may eventually result in speciation (the emergence of new species, macroevolution). In other words, natural selection is a key process in the evolution of a population.

Natural selection is a cornerstone of modern biology.
@Daniel_Fishe, @03Cobra, @mitchellmckain, @gbrooks9, @davecarlson

Since I did not receive much satisfaction form @T_aquaticus and @glipsnort, I decided to inquire once more to the Wikipedia, which is constantly updating its entries and above is what I found. It says that natural selection is the result of the environment interacting with the phenotype to create new biological forms or species. It is the cornerstone of modern biology. There is nothing random or stochastic here.

51

Heritable traits in a reproducing population is what causes neutral drift.

The last part of your definition explained it the best, “may not be predicted precisely”.

Let’s say a new mutation gives individuals within a species 10% better camouflage compared to other alleles for the same gene. Does this mean only individuals with that advantageous mutation will reproduce? No. You can’t precisely predict how many offspring each individual will have based on which alleles they have. On average, the individuals with the advantageous allele will have more offspring, but it’s not a guarantee for every single individual.

ABE:
Over the last 20 years I have done a lot of protein chromatography, and it is a really cool example of selective stochastic processes in action. Proteins will elute off of size exclusion columns according to their size, with bigger proteins coming off the column before smaller ones. The reason for this is the smaller proteins have a higher probability of entering the small pores in the beads that make up the column. This is a stochastic process, and the shape of the peaks coming off the column are Gaussian curves:

image

Natural selection filters alleles in much the same way.

The interaction between environment and phenotype is stochastic in the way I described above.

52

Amino acid coding has similar bias to DNA and thus is more likely to produce a change that is less significant. Besides synonymous substitutions, the codons for amino acids with similar properties tend to be more similar to each other. Bias in synonymous codons is rather common in mitochondrial genomes.

Mutations are random in the looser sense of “humanly unpredictable” as well as in the mathematical sense of “best described by a probability function”. The randomness relative to resulting fitness, already discussed, is important to recognize as well. But there are certainly gene regions that have much higher rate of mutation than others. Some genes need to be variable, such as the ones coding for antibodies.

53

I guess it depends on how back you want to go and ect… but I essentially explain the evolutionary process like this.

We live in a world with billions of niches. Some animals just happen to have something that helps them with that niche. Because they have that ecological connection it allows one or both of them to do really s well. They spread their genes better and those genes get spread more and more until it’s a basal trait among its descendants and that basal trait will also turn out to be better at other things as it’s more refined. That creates new ecological niches. Some of the mutations are more morphologically focused snd some are more process focused. Such as if among some white flowers there happens to be one with twice as large of petals. These petals allow more insects to land on it. Over time those start to do good. While this is happening another one of the same species just happens to have extra sticky pollen. This pollen helps its genetics get spread more to other plants and after a able many have these traits. Another in the same species happened to bloom a few weeks earlier. That one gets a head starts on blooming and ends up being pollinated well. The one with sticky pollen ends up having an offspring with a very narrow flower. A species of flies land on it. It’s too tiny for them to make it down to the nectar and pollen but a few runt examples of its species can. Over time those are able to feed easier and so they end up doing it again and again.

54

Word salad meaning nothing. As I said before4, if you do not know what is the cause, then just admit it.

On the other hand if you agree with Dawkins that life and reality are without meaning, then it follows that science is without meaning and to prove it you sabotage it to make it meaningless.

So now random ,means “may not be predicted precisely.” The biggest problem with this view is that we now know that few if any processes can be predicted precisely which makes everything random. If everything is rando\m, then then the concept is meaningless and science itself is meaningless.

Another serious problem is that random does not mean “not predictable.” Some process may be not predictable because it is random, but there are other reasons why they are not predictable. When you conflate the meaning of one word with other words you lose the original meaning of the word, which is not hood because random is a good word with a good meaning.

Science has the task of observing and understanding nature. Philosophy has the task of determining the meaning of words and the meaning of nature.

The question I raised was not if natural selection could be predicted or not. The question was whether on not ecology was the cause or agent behind natural selection as indicated in the Wiki article. If it is, then natural selection is not random in relationship to the ecology, even if it cannot be calculated precisely.

You says that a mutation gives some a 10% advantage. Do individuals have a sign on their backs? Of course not. It is natural selection which determines if some will survives and flourish while other do not. It is unpredictable because it is complicated with many factors that may not be visible, not because some of our predictions are wrong, but we do know that those which survive and flourish will do so because they have an ecological advantage.

ABE ?

There is no evidence for this. What is the result of this interesting phenomenon?

Where are the Gaussian curves in natural selection?

Where is the evidence, since science is a evidence based process?

This is not a coincidence. Every biota is born into a niche. They are born of a species that has already been selected into existence. If an individual has a mutation that helps it survival in that niche or a new home niche, then good for them. Most individuals are little different from the others, and try to make the most of what they have.

Individuals do not try to spread their genes, but since there are many offspring, a small advantage can make a significant difference both ways. Ecology is made up of many factors, physical such as climate, as well as plants, bacteria, insects, animals, and humans.

@paleomalacologist, David, thank you for the comments.

You of course are talking about genes and variation, while I am core concerned about natural selection which seems to be misunderstood. I really do not understand how Darwin’s theory of natural selection has been around for more than 150 years and yet we do not know how it works, so we do not know if it works. .

55

More lottery tickets are sold when the jackpot is higher, but the lottery is still random. Lottery drawings happen at the same time each week, yet the lottery is still random.

56

It isn’t word salad. Heritable traits in reproducing populations is what causes neutral drift. When traits are being passed on in a limited population then there are going to be winners and losers among the different alleles. Some will die out, some will continue on at low frequency, and some will increase in frequency. None of this requires natural selection.

That is what stochastic means, per your definition.

Again, I define them as stochastic.

All I am asking is that you try to work through my example. Here it is again:

Let’s say a new mutation gives individuals within a species 10% better camouflage compared to other alleles for the same gene. Does this mean only individuals with that advantageous mutation will reproduce? No. You can’t precisely predict how many offspring each individual will have based on which alleles they have. On average, the individuals with the advantageous allele will have more offspring, but it’s not a guarantee for every single individual.

There’s no evidence for natural selection?

The Gaussian curves would be the number of offspring relative to other individuals without the allele.

57

Yes; this remains random in the sense of being probabilistic, but the distribution of probabilities is uneven over the genome. This does mean that certain types of mutations are more likely than others. Similarly, exon shuffling (mixing functional pieces of existing genes) is more likely to produce a protein that does something than simply throwing together a random sequence of amino acids.

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58

Random has a range of meanings, and needs to be clarified. Natural selection is, of course very non-random in its directionality. But it has aspects that may reasonably considered random as well. For example, what genetic variations are available for the selection to operate upon - that is determined by a probabilistic process. Catastrophic selection is basically a case of being in the wrong place at the wrong time through no fault of the organism, e.g. being where an asteroid crashes in; again, that can reasonably described as random in some senses. Given a tightly controlled setup, the course of natural selection can be predicted, such as in lab competition between flour beetles or introducing the same kind of animals to a similar environment. But we’re particularly interested in the course of evolution in the setting of the entire Earth, which has rather more variables to track.

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59

Another way to put it is that randomness requires context. You need to describe the variables involved in order for the description to make sense. This is why mutations are described as being random with respect to fitness, and that definition is based on the early work done by Luria, Delbruck, and the Lederbergs that I described in the opening post. To stress the point again, the discovery of randomness in mutations occurred before the structure of DNA was known.

I agree with others that features like codon usage do tilt mutations away from being deleterious. However, it could be equally argued that non-conservative change (e.g. nonpolar to charged amino acid) at a specific protein residue could be beneficial in some situations.

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60

According to Darwin’s Theory it all is based on natural selection. Even though Darwin’s Theory has it s problems here it is definitely correct. It is very strange that the science seems to be rejecting Darwin today.

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No that is what it means according to your “scientific” definition.

Defining something as “stochastic” does not make them stochastic. Nor does saying something cannot not be predicted precisely make it random. Circular thinking is not the basis of sound thinking.

Prediction is not the question, causation is is the issue. A new mutation is not selected in because it is 10% or a 29% better camouflaged. It is selected in because it is better adapted to its environment than its peers, and that is determined by life and not by math.

Todays’ science seems to confuse math with life/reality. Life and Reality have meaning and purpose. Math does not. Math is not science, because science is about life.