Amount of variation in gene mutation and/or in copying error

[timf1234]

Hi folks,

I am Tim from Texas. My turning point was when at the age of 17, I conclusively figured out that there is No Free will what so ever. Rest of the thing was easy.
I have posted polls after polls at many atheist websites and discovered only 25% of all atheists believe there is No Free Will. After a lot of convincing this numbers goes up to 35% or so.
I discovered that it is relatively easy to figure out and digest that there is no god but it is a lot harder to understand and digest that we have no free will.

I have to know the answer to the following questions.
I will be very thankful to you if you can explain.

1) As I know, Evolution = small variation in DNA code + Natural selection -> then repeat.
Is this small variation in Gene 100% random or has some constraint attached to it?
For example, a large and smart software code consist of higher level language, let's say, graphical user interface (GUI) in the highest level - let’s say level 1 or L1.
Zooming in to the code shows, let's say Java or C #code - let's call it level 2 or L2.
Zooming in further shows Assembly language code, let's call it L3, Zooming in further shows 1's and 0's, L4.
If this software were analogous to the DNA Code then does the gene mutation allows any bit to be changed or only words could be changed at higher level like L1 or L2 level but not at lower levels, say L3 or L4?
Note: Not all sequence of 1’s and 0’s are allowed in Assembly language. Some sequence won’t make sense. Not all 4 byte sequence are used to build Assembly language codes. There are unused 4 byte sequence in Assembly language.

Another example:
If we assume library of congress represent the code in DNA then
Is it allowed to change any character in the library of congress fully randomly or the constraint is that change has to be a dictionary word? Not all sequence of characters creates valid English dictionary word.

If genetic mutation is a free for all, 100% random change without any constraint then it is very hard for me to believe that we could have this successful complex life out of 100% random changes and natural selection. But randomness with some constrain could produce variety of complex life.

Also please confirm my understanding that any learned behavior like fast swimming, strengthening of muscle by practice can't be transferred to offspring via gene.

Please confirm that only random genetic mutation can come via Heisenberg Uncertainty principle. Anything else is caused.

My 2nd question is about Photon.
2. If we release single electron to freely fall anywhere on a wall full of photo censors then this single electron can strike any of the thousands of censors on the wall. If we repeat the experiment millions of time then each photo cell will get more or less equal number of photon.
Could this be interpreted as: each photon knows where the previous photons struck? And that photon tries to maintain statistical equal average for each censor? EPR paradox like stuff – particle communicates instantaneously – Infinite velocity?

 

[RecoveringYuppy]

Is this small variation in Gene 100% random or has some constraint attached to it?

Mutations are known to not be "100% random". In particular there are areas in the DNA where mutations happen more often. There are also particular types of mutations which happen such as repeititions (which probably has some biological name I'm forgetting now).

 

[DallasDad]

If we have no free will, you have no choice about presenting your argument, and I have no choice about accepting it or rejecting it. The argument itself, therefore, is irrelevant, and you might as well just chant "Cheerios! Cheerios!" at me.

 

[Reality Check]

Hi My 2nd question is about Photon.
2. If we release single electron to freely fall anywhere on a wall full of photo censors then this single electron can strike any of the thousands of censors on the wall. If we repeat the experiment millions of time then each photo cell will get more or less equal number of photon.
Could this be interpreted as: each photon knows where the previous photons struck? And that photon tries to maintain statistical equal average for each censor? EPR paradox like stuff – particle communicates instantaneously – Infinite velocity?

If you detect photons in a wall of photodetectors and they are detected in random places then obviously they were fired at random places.
In order to get a non random distribution then you have to do things like the double-slit experiment.
The EPR paradox is a different situation.

 

[Wowbagger]

I conclusively figured out that there is No Free will what so ever.

I am mildly curious to know how you came about that conclusion.

Is this small variation in Gene 100% random or has some constraint attached to it?

The more we understand about how genes vary, the smaller percentage of it is deemed "random".

If we knew nothing at all, it would be 100%. The more we study the specifics in how recombination works, in how single point mutations happen, in how transposons jump around, etc; the less random it gets. If we knew everything, it might be 0% (assuming quantum uncertainty is not significant in large scales).

If this software were analogous to the DNA Code then does the gene mutation allows any bit to be changed or only words could be changed at higher level like L1 or L2 level but not at lower levels, say L3 or L4?

Well, software is only analogous to DNA in very broad terms. The more detailed you get into it, the less analogous it becomes.

Intelligent Design proponents might claim that DNA is a code or a language, but all they are really doing is taking an analogy far too literally, and not developing any innovations out of that.

Evolutionary biologists might also talk about DNA as a code, but they do not use that analogy as the basis for their work. They recognize it as merely an easy-to-use communication tool.

Most of the innovative discoveries about how DNA originated came from scientists who recognized DNA as NOT a code, but a self-replicating molecule, almost like a crystal-of-sorts. If it looks like code to us, it is only a consequence of the patterns those molecules ended up replicating themselves into.

Note: Not all sequence of 1’s and 0’s are allowed in Assembly language. Some sequence won’t make sense. Not all 4 byte sequence are used to build Assembly language codes. There are unused 4 byte sequence in Assembly language.

There would also be a lot of coding patterns that might not make sense in the context of DNA and genes. But, this gets awfully complicated, and I do not, yet, have a pithy way of explaining it.

Perhaps you should pick up a good book on Evo-Devo.

If genetic mutation is a free for all, 100% random change without any constraint then it is very hard for me to believe that we could have this successful complex life out of 100% random changes and natural selection. But randomness with some constrain could produce variety of complex life.

It is NOT randomness that creates complexity. Randomness has no power, here! It is the selection algorithm that does all the heavy lifting. In this case, it is Natural Selection.

You could say that, in a sense, it is the filtering action of Natural Selection that is the constraint. But, that might oversimplify things a little.

(ETA: Physics, itself, also places a slew of constraints on the system.)

Perhaps a good book on evolutionary computer simulations will get you used to the concepts of where the power of selection algorithms comes from.

Also please confirm my understanding that any learned behavior like fast swimming, strengthening of muscle by practice can't be transferred to offspring via gene.

Acquired characteristics, that is: Traits one acquired during their own lifetime, from their own experiences and training; cannot be transferred to genes.

But, if the appropriate selection pressures are applied, along with the right mix of genetic variety, you could get species that, in general, move faster and faster, or are stronger and stronger, in certain ways, over time.

Please confirm that only random genetic mutation can come via Heisenberg Uncertainty principle. Anything else is caused.

Eh, that really depends on how you define "random".

I think it is more useful not to focus so much on randomness. Remember: It has no true power here! But, focus more on the mechanics of how evolutionary processes work. Getting hung up on the randomness seems counter-productive to me, unless you really have a hankering to specialize in that area.

 

[timf1234]

Wowbagger,

Your response was very helpful. Thank you.
Yes I agree with you that natural selection works like a filter. However, if there is no change in the gene then there is nothing new to filter from. So mutation (small changes) is necessary for evolution. Then the question comes in how this mutation is taking place.
Is it caused? Os it pre-determined? Whether we know the exact cause or not is a separate story. As long as it is caused then it is not random. True randomness is via Heisenberg uncertainty principle only.

Now, I am thinking, changes in the gene while copying or even spontaneous genetic mutation is not truly random.
What theist are saying, if it is not random then it is designed.
I can argue even if it is not random how do we know who designed it and what are his (god's) characteristic. No way to tell that.

You asked me about how did I concluded that there is no Free will.
I thought in two steps.

Step 1: I kept quantum mechanics out. In the absence of randomness everything was determined at the time of big bang because the Universe is governed by strict laws.

Step 2: I brought in the quantum mechanics. Now I can't say that everything was determined at the time of the big bang but has wiggle room as allowed by Heisenberg Uncertainty Principle. But we have no control in that wiggle room. Therefore, we still do not have free will.

What I do is cause by my thought. My thought is caused by electrochemical activity in my neurons. Each and every molecules, particles in my brain, in my body, and outside must follow strict laws therefore, we have no free will.,

 

[timf1234]

If we have no free will, you have no choice about presenting your argument, and I have no choice about accepting it or rejecting it. The argument itself, therefore, is irrelevant, and you might as well just chant "Cheerios! Cheerios!" at me.

DallasDad,

Watch this. Best video on free will. Can you digest it?

http://video.google.com/videoplay?docid=1022039654662139670#

 

[timf1234]

If you detect photons in a wall of photodetectors and they are detected in random places then obviously they were fired at random places.
In order to get a non random distribution then you have to do things like the double-slit experiment.
The EPR paradox is a different situation.

A free single photon can land anywhere it choses.
Please check out Hiseinberg Uncertainty Principle (HUP)

 

[Dancing David]

A free single photon can land anywhere it choses.
Please check out Hiseinberg Uncertainty Principle (HUP)

Not really what HIP says , okay? (In short HIP says the more you know about one component of the the particle's momentum vector, the less you may know about another component. Now there are quantum reasons that may not constrain the position of a particle but then there is a probability that can be potentially discussed.)

Now as to variation and natural seelction.

There are multiple paths to variation in the genome and its expression in phenotypes. There are sometimes multiple alleles that are invoved in an expressed trait, there are genes and allele sets that control the expression of ther genes.

This leads to considerable variation without any need for the 'mutation', then there are genes thats eem to point to other places in the genetic data and so they can direct the mechanism to use other areas of the 'code' than were being used before.

 

[Dancing David]

Wowbagger,

Your response was very helpful. Thank you.
Yes I agree with you that natural selection works like a filter. However, if there is no change in the gene then there is nothing new to filter from. So mutation (small changes) is necessary for evolution. Then the question comes in how this mutation is taking place.
Is it caused? Os it pre-determined? Whether we know the exact cause or not is a separate story. As long as it is caused then it is not random. True randomness is via Heisenberg uncertainty principle only.

Now, I am thinking, changes in the gene while copying or even spontaneous genetic mutation is not truly random.
What theist are saying, if it is not random then it is designed.
I can argue even if it is not random how do we know who designed it and what are his (god's) characteristic. No way to tell that.

You asked me about how did I concluded that there is no Free will.
I thought in two steps.

Step 1: I kept quantum mechanics out. In the absence of randomness everything was determined at the time of big bang because the Universe is governed by strict laws.

Step 2: I brought in the quantum mechanics. Now I can't say that everything was determined at the time of the big bang but has wiggle room as allowed by Heisenberg Uncertainty Principle. But we have no control in that wiggle room. Therefore, we still do not have free will.

What I do is cause by my thought. My thought is caused by electrochemical activity in my neurons. Each and every molecules, particles in my brain, in my body, and outside must follow strict laws therefore, we have no free will.,

Perhaps 'causal' is different than 'determined'.

 

[sphenisc]

A free single photon can land anywhere it choses.

Therefore a photon has free will.

We have photons - therefore we have free will.

QED

 

[drkitten]

1) As I know, Evolution = small variation in DNA code + Natural selection -> then repeat.
Is this small variation in Gene 100% random or has some constraint attached to it?
For example, a large and smart software code consist of higher level language, let's say, graphical user interface (GUI) in the highest level - let’s say level 1 or L1.
Zooming in to the code shows, let's say Java or C #code - let's call it level 2 or L2.
Zooming in further shows Assembly language code, let's call it L3, Zooming in further shows 1's and 0's, L4.
If this software were analogous to the DNA Code then does the gene mutation allows any bit to be changed or only words could be changed at higher level like L1 or L2 level but not at lower levels, say L3 or L4?
Note: Not all sequence of 1’s and 0’s are allowed in Assembly language. Some sequence won’t make sense. Not all 4 byte sequence are used to build Assembly language codes. There are unused 4 byte sequence in Assembly language.

That's an amazingly bad analogy and I would drop it.

Mutations, by definition, are changes to the DNA, but there are lots of different types. For example, you can simply substitute one base for another (a T for a C), you can delete an entire segment of DNA consisting of up to thousands of bases, or duplicate a segment so that it occurs twice occurs twice in the string.

If we assume library of congress represent the code in DNA then
Is it allowed to change any character in the library of congress fully randomly or the constraint is that change has to be a dictionary word? Not all sequence of characters creates valid English dictionary word.

There's no such thing as a "dictionary word" in DNA.

If genetic mutation is a free for all, 100% random change without any constraint then it is very hard for me to believe that we could have this successful complex life out of 100% random changes and natural selection.

Ah. Argument by incredulity. Not a good start.

Also please confirm my understanding that any learned behavior like fast swimming, strengthening of muscle by practice can't be transferred to offspring via gene.

No, but a tendency to learn the behavior quickly and with minimal training can, which can result in apparently "learned" behavior evolving. Richard Dawkins has a very good discussion of this in The Ancestor's Tale in the section describing the upside-down catfish.

Please confirm that only random genetic mutation can come via Heisenberg Uncertainty principle.

I can't "confirm" that because it's not right. It's not even wrong.

2. If we release single electron to freely fall anywhere on a wall full of photo censors then this single electron can strike any of the thousands of censors on the wall. If we repeat the experiment millions of time then each photo cell will get more or less equal number of photon.

Why should you assume that? Electron beams can be focused just as light beams can. How do you think an old-style CRT television works?

Could this be interpreted as: each photon knows where the previous photons struck?

No. Even if you specifically set up an electron gun that gave you uniform distribution, there's no notion of "knowing," any more than a die "knows" what the previous numbers it rolled were.

This is a famous error called "the gambler's fallacy."

 

[Wowbagger]

Mutations, by definition, are changes to the DNA, but there are lots of different types. For example, you can simply substitute one base for another (a T for a C), you can delete an entire segment of DNA consisting of up to thousands of bases, or duplicate a segment so that it occurs twice occurs twice in the string.

Oh yeah! First thing I wanted to say, tim1234, was that you should probably study much more of this site:
http://evolution.berkeley.edu/evolibrary/home.php

It is very good!

However, if there is no change in the gene then there is nothing new to filter from.

There are many different ways in which DNA and genes can vary, over time. Not just single-point mutations. There are also transposons ("jumping genes"), recombination, duplications, etc.

The rate of evolvability, itself is evolvable. Systems that replicate themselves in a manner that is flexible enough to provide a good level of variety, without immediately detrimental effects, will generally outlast the competition.

You asked me about how did I concluded that there is no Free will.
I thought in two steps.

Step 1: I kept quantum mechanics out. In the absence of randomness everything was determined at the time of big bang because the Universe is governed by strict laws.

Step 2: I brought in the quantum mechanics. Now I can't say that everything was determined at the time of the big bang but has wiggle room as allowed by Heisenberg Uncertainty Principle. But we have no control in that wiggle room. Therefore, we still do not have free will.

What I do is cause by my thought. My thought is caused by electrochemical activity in my neurons. Each and every molecules, particles in my brain, in my body, and outside must follow strict laws therefore, we have no free will.,

I think the reason a lot of skeptics still accept Free Will is because denial of it assumes too much. For example: You are assuming something must either be: completely deterministic OR quantum-level random but uncontrollable. But, no one has presented empirical evidence that this dichotomy is real.

Every skeptic has their own ideas about the nature of Free Will. And, until we develop a complete, empirical explanation for how we seem to have free will; that can satisfactorily answer all or most of our questions on the subject; I see no reason to completely dismiss the concept as merely an illusion. Yet.

(NOTE: The rest of this post is not, strictly speaking, science.)
I have no evidence of a third option, between that dichotomy. But, I do have an imagination. And, I can imagine different ways Free Will could emerge from the interactions of a complex network of systems, that are partly deterministic, and partly random (quantum or otherwise). Some pieces acting more directly on each other, than others. What might come out of this could be genuine opportunities for free choice, that would not violate anything we know about physics. But, I digress. The mad scientist portions of my brain need to get back to sleep.

 

[blutoski]

My 2nd question is about Photon.
2. If we release single electron to freely fall anywhere on a wall full of photo censors then this single electron can strike any of the thousands of censors on the wall. If we repeat the experiment millions of time then each photo cell will get more or less equal number of photon.
Could this be interpreted as: each photon knows where the previous photons struck? And that photon tries to maintain statistical equal average for each censor? EPR paradox like stuff – particle communicates instantaneously – Infinite velocity?

No. You're assuming that the result of a random sequence of hits will be an even [permutation].

This is a common misunderstanding about random number sequences.

As a consequence, humans are really, really, bad at generating 'random' number sequences. We keep trying to even things up to what we expect are the right ratios.

There was another thread that discussed a stats prof who would leave the classroom and have one half 'invent' a random sequence and the other half flip a coin for a genuine random sequence. He was able to identify which was which pretty easily.

 

[blutoski]

1) As I know, Evolution = small variation in DNA code + Natural selection -> then repeat.
Is this small variation in Gene 100% random or has some constraint attached to it?
For example, a large and smart software code consist of higher level language, let's say, graphical user interface (GUI) in the highest level - let’s say level 1 or L1.
Zooming in to the code shows, let's say Java or C #code - let's call it level 2 or L2.
Zooming in further shows Assembly language code, let's call it L3, Zooming in further shows 1's and 0's, L4.
If this software were analogous to the DNA Code then does the gene mutation allows any bit to be changed or only words could be changed at higher level like L1 or L2 level but not at lower levels, say L3 or L4?
Note: Not all sequence of 1’s and 0’s are allowed in Assembly language. Some sequence won’t make sense. Not all 4 byte sequence are used to build Assembly language codes. There are unused 4 byte sequence in Assembly language.

Another example:
If we assume library of congress represent the code in DNA then
Is it allowed to change any character in the library of congress fully randomly or the constraint is that change has to be a dictionary word? Not all sequence of characters creates valid English dictionary word.

Yes, but fortunately nature is not like books which require perfect grammar and spelling to work. Organisms appear to be all about 'good enough/close enough'. Many substitutions do not change the codon. (this is called Wobble base pair^WP) and many changed codons do not alter the properties of the resulting protein in the current environment. These are called silent mutations^WP.

Another disanalogy is genetic scaffolding. A library could handle misspellings better if it had multiple copies of a book. By the same token, many genes are duplicated thousdands of times in the genome. Radical changes in one copy merely become the potential for a new trait, without the loss of the old trait.

If genetic mutation is a free for all, 100% random change without any constraint then it is very hard for me to believe that we could have this successful complex life out of 100% random changes and natural selection. But randomness with some constrain could produce variety of complex life.

I don't see why.

There are different kinds of mutations and some are more likely than others, but these different mechanisms don't translate into mutations being more likely to be beneficial or harmful. That's a function of the allele's relationship to the environment.

To provide a concrete example: my ability to breathe air is a beneficial allele on land. It's not such a benefit at the bottom of a lake.

Also please confirm my understanding that any learned behavior like fast swimming, strengthening of muscle by practice can't be transferred to offspring via gene.

Basically, although there are some suggestions that acquired immunological properties can be propagated across generations in some organisms in certain situations. However, this makes sense based on the mechanism, and cannot be generalized to other acquired abilities.

Please confirm that only random genetic mutation can come via Heisenberg Uncertainty principle. Anything else is caused.

? These concepts are unrelated. I think you misunderstand HUP. HUP is not about randomness. Picture it as two-dimensional error bars for measurements.

 

[blutoski]

Yes, but fortunately nature is not like books which require perfect grammar and spelling to work. Organisms appear to be all about 'good enough/close enough'. Many substitutions do not change the codon. (this is called Wobble base pair^WP) and many changed codons do not alter the properties of the resulting protein in the current environment. These are called silent mutations^WP.

Sorry: what I meant by this is that every mutation still contains valid codons. Every combination of base pairs is a 'word' in your library analogy.

 

[Paul C. Anagnostopoulos]

If we have no free will, you have no choice about presenting your argument, and I have no choice about accepting it or rejecting it. The argument itself, therefore, is irrelevant, and you might as well just chant "Cheerios! Cheerios!" at me.

You missed the memo that said we're supposed to pretend.

~~ Paul