Evolution My ToE

[Hockeycowboy]

In Genesis (also some ancient history) men lived far far longer than they do today. So I allow for the possibility that perhaps the different laws of nature resulted in DNA behaving somewhat differently.

That’s a reasonable assumption, with which I agree!

We have no idea how perfect DNA would appear.

It seems our telomeres, on the ends of our chromosomes, get shorter with age. (Maybe that has some effect?)
Now, what if these telomeres didn’t get shorter, but always kept their length?

There is a paper on just such a study...can’t remember where I read it. It might be online.

 

[shunyadragon]

Traits that produce successful offspring?
You see right there. Your language seems no different to his.
"Traits" are passed on through heredity. They vary - good, bad, ugly.
You are only causing me to repeat...
Some tend to think of natural selection as an all-powerful force, urging organisms on, constantly pushing them in the direction of progress, but this is not what natural selection is like at all.

Natural selection is not all-powerful; it does not produce perfection. If your genes are "good enough," you'll get some offspring into the next generation. You don't have to be perfect. This should be pretty clear just by looking at the populations around us: people may have genes for genetic diseases, plants may not have the genes to survive a drought, a predator may not be quite fast enough to catch her prey every time she is hungry. No population or organism is perfectly adapted.


Remember, the cabbage for example was selected by the farmer, because it did well, and it had the features he wanted.
Left to reproduce, that cabbage will not now only produce bigger, better, best.
The good, bad, and ugly, will be part of the process.
The farmer, however, is there to again select the best, and discard the rest.
With natural selection, it doesn't care about the imperfections. It's a mindless concept.
So while there are positives, there are negatives also, and some of those negatives do stick around. We have many examples, don't we?


This of course happen in some cases, I agree.
However, I get the impression that, for some persons, it is applied in every case, and to every thing... like a wave of a magic wand.


I have my ideas. It's not really the narrator's fault.
I'm not getting the natural selection concept to work as it appears to be magical in some areas... Not all. Some.

Nothing in this rambling rant relates to the science of evolution.

Dunning-Kreuger effect, and a dose of the Peter Principle. is at work here

 

[shunyadragon]

That’s a reasonable assumption, with which I agree!

We have no idea how perfect DNA would appear..

DNA has never been prefect.

[quote[ It seems our telomeres, on the ends of our chromosomes, get shorter with age. (Maybe that has some effect?)
Now, what if these telomeres didn’t get shorter, but always kept their length?

Confusingly false.

There is a paper on just such a study...can’t remember where I read it. It might be online.

Look in the outhouse. Your paper comes in perforated rolls, or a SEARS book from the last century.

 

[Jose Fly]

Okay. Continuing...
So because an error occurs during replication, that does not mean it will automatically be a mutation.
However, it can be a mutation - one that has been repaired though not perfectly.

Can you clarify what you mean by "repaired though not perfectly"?

If this is the case, sometimes the mutated gene can still function, and be recognized by communicating genes, as the gene that carries out X function. Or... to be continued...

So far, is there anything you disagree with, or don't understand?

Do you have an example of what you're talking about?

 

[nPeace]

Can you clarify what you mean by "repaired though not perfectly"?


Do you have an example of what you're talking about?

Sure.
Mutations can also be caused by exposure to specific chemicals or radiation. These agents cause the DNA to break down. This is not necessarily unnatural — even in the most isolated and pristine environments, DNA breaks down. Nevertheless, when the cell repairs the DNA, it might not do a perfect job of the repair. So the cell would end up with DNA slightly different than the original DNA and hence, a mutation.

The error in the gene (I should have been more specific) is repaired, though not perfectly. There are examples, I came across of the different results, but I would have to search for that again.
You can always search on line for some of the different results after repair.

However, this is due to errors caused by environmental damage.
With replication error, I know most errors are fixed due to the mechanism in place...
Proofreading (biology) - Wikipedia
In bacteria, all three DNA polymerases (I, II and III) have the ability to proofread, using 3’ → 5’ exonuclease activity. When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA and excises the mismatched base. Following base excision, the polymerase can re-insert the correct base and replication can continue.
However, in some cases, it would be expected that a perfect job is not always possible, and yes, some mutations do get through (We'll get into the mutation rates later, if you believe that's still important).

Examples of partially repaired mutations and functionality if that's what you are asking.
Diagram from link below.
You will find the below information under the diagram on this link.

Spoiler: Extract

We performed similar electrophysiological analyses on cells transfected with plasmids encoding the active or inactive ribozyme and EGFP as a reporter. Only EGFP-positive cells were tested. Figure Figure4,4, c–f, illustrates representative “tail” currents from a wild-type cClC-1 cell, a T268M cell, and two ribozyme-transfected cells. In this experiment, tail currents were measured at a test potential of –120 mV (arrow in Figure Figure44 inset) and represent the activity of channels opened by the preceding voltage. The bold black line in each family of traces represents the tail current recorded after a 1.4-second prepulse to 0 mV. In wild-type cClC-1–expressing cells (Figure (Figure4c),4c), channels are fully activated at this potential, while very little channel activation (∼13%) occurs in T268M-expressing cells (Figure (Figure4d).4d). In Figure Figure4,4, e and f, current traces obtained from two ribozyme-expressing cells illustrate a spectrum of biophysical rescue with either complete (Figure (Figure4e)4e) or partial (about 40% activation, Figure Figure4f)4f) restoration of wild-type chloride channel function.

We evaluated the degree of functional restoration in several individual cells by examining the voltage dependence of activation and determining the voltage at which half-maximal activation (V1/2) occurs (Figure (Figure5).5). We categorized the magnitude of repair as full, partial, or none based upon the observed changes in V1/2 (Figure (Figure5a).5a). Full repair was defined as V1/2 falling within 5 mV of wild-type cClC-1, a value well within one SD of the mean. No repair was defined as V1/2 values falling within two SDs (approximately 18 mV) of the mean of T268M. The remaining values were considered indicative of partial repair (i.e., a mixed population of mutant and corrected channels). Thirteen of 71 ribozyme-transfected cells (18%) exhibited a significant shift of V1/2 to more negative potentials. Two of these cells demonstrated a complete shift in the activation curve to voltages that are not significantly different from wild-type cClC-1, suggesting that the trans-splicing ribozyme has the ability to fully rescue the mutant phenotype.

I haven't thoroughly search this. I was merely reasoning from commonsense and logic, but I can look into it more if you like.

 

[SkepticThinker]

Apparently you are not familiar with bible prophesy. John was taken to the future and wrote what he saw and heard.

So how do we verify that a person travelled to the future?

 

[SkepticThinker]

I asked a question. If anyone claims DNA was the same, and therefore could be used to tell us about where man came from, they would need to show that God created us with the same nature (therefore DNA) as we see today. More a science issue than 'fundy' issue.

You're going to have to demonstrate that some god exists first, before we start attributing actions to it.

 

[SkepticThinker]

Great, so when we see spirtits as rulers or influencing ancient history you dismiss it because you believe there is no such thing. That is denial. Furthermore denial based on ignorance alone.

When and where do we see "spirits as rulers or influencing ancient history?"
Perhaps people dismiss it because there is no good evidence of such things. Have you presented any?

 

[SkepticThinker]

Possibly, if they were a created kind, but we don't know that to be the case. Man WAS here days after the sea creatures was created, so if the crabs underwent evolving at all, it is likely that horseshoe crabs actually came after man. We'd have to look at the deposits that the earliest horseshoe crabs were found in. Ha.

No, how would I know what original kinds they came from or were? You can't just make stuff up here as if you know something.

Spirits lived with me, trees grew in weeks, and man lived about 1000 years. That qualifies as different to me.

You should since you're the one trying to push it as some kind of fact of reality.

 

[Jose Fly]

Sure.

Thanks!

Mutations can also be caused by exposure to specific chemicals or radiation. These agents cause the DNA to break down. This is not necessarily unnatural — even in the most isolated and pristine environments, DNA breaks down. Nevertheless, when the cell repairs the DNA, it might not do a perfect job of the repair. So the cell would end up with DNA slightly different than the original DNA and hence, a mutation.

The error in the gene (I should have been more specific) is repaired, though not perfectly. There are examples, I came across of the different results, but I would have to search for that again.
You can always search on line for some of the different results after repair.

Okay. Specific examples of what you're talking about would indeed be very helpful.

However, this is due to errors caused by environmental damage.

Yep.

With replication error, I know most errors are fixed due to the mechanism in place...
Proofreading (biology) - Wikipedia
In bacteria, all three DNA polymerases (I, II and III) have the ability to proofread, using 3’ → 5’ exonuclease activity. When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA and excises the mismatched base. Following base excision, the polymerase can re-insert the correct base and replication can continue.
However, in some cases, it would be expected that a perfect job is not always possible, and yes, some mutations do get through (We'll get into the mutation rates later, if you believe that's still important).

And you are aware that they are limited in the type of replication errors they can fix, right? As that Wiki page notes, in bacteria it repairs nucleotide mismatches (e.g., substituting adenosine for guanine), which means if the mutation is not a mismatch it won't fix it.

And yes, given our earlier discussion I think mutation rates will be important.

Examples of partially repaired mutations and functionality if that's what you are asking.
Diagram from link below.
You will find the below information under the diagram on this link.

Spoiler: Extract

We performed similar electrophysiological analyses on cells transfected with plasmids encoding the active or inactive ribozyme and EGFP as a reporter. Only EGFP-positive cells were tested. Figure Figure4,4, c–f, illustrates representative “tail” currents from a wild-type cClC-1 cell, a T268M cell, and two ribozyme-transfected cells. In this experiment, tail currents were measured at a test potential of –120 mV (arrow in Figure Figure44 inset) and represent the activity of channels opened by the preceding voltage. The bold black line in each family of traces represents the tail current recorded after a 1.4-second prepulse to 0 mV. In wild-type cClC-1–expressing cells (Figure (Figure4c),4c), channels are fully activated at this potential, while very little channel activation (∼13%) occurs in T268M-expressing cells (Figure (Figure4d).4d). In Figure Figure4,4, e and f, current traces obtained from two ribozyme-expressing cells illustrate a spectrum of biophysical rescue with either complete (Figure (Figure4e)4e) or partial (about 40% activation, Figure Figure4f)4f) restoration of wild-type chloride channel function.

We evaluated the degree of functional restoration in several individual cells by examining the voltage dependence of activation and determining the voltage at which half-maximal activation (V1/2) occurs (Figure (Figure5).5). We categorized the magnitude of repair as full, partial, or none based upon the observed changes in V1/2 (Figure (Figure5a).5a). Full repair was defined as V1/2 falling within 5 mV of wild-type cClC-1, a value well within one SD of the mean. No repair was defined as V1/2 values falling within two SDs (approximately 18 mV) of the mean of T268M. The remaining values were considered indicative of partial repair (i.e., a mixed population of mutant and corrected channels). Thirteen of 71 ribozyme-transfected cells (18%) exhibited a significant shift of V1/2 to more negative potentials. Two of these cells demonstrated a complete shift in the activation curve to voltages that are not significantly different from wild-type cClC-1, suggesting that the trans-splicing ribozyme has the ability to fully rescue the mutant phenotype.

I haven't thoroughly search this. I was merely reasoning from commonsense and logic, but I can look into it more if you like.

I'm not sure what that paper has to do with our current discussion, since it's about geneticists attempting to restore genetic function (protein production) via gene therapy. IOW, it's not really about natural DNA repair, and is instead about people trying to find ways to fix broken genes through our own intervention.

But, I don't want to unnecessarily bog this discussion down, so if you'd rather continue presenting your scenario, I'm fine with that.

 

[nPeace]

Thanks!


Okay. Specific examples of what you're talking about would indeed be very helpful.


Yep.


And you are aware that they are limited in the type of replication errors they can fix, right? As that Wiki page notes, in bacteria it repairs nucleotide mismatches (e.g., substituting adenosine for guanine), which means if the mutation is not a mismatch it won't fix it.

And yes, given our earlier discussion I think mutation rates will be important.


I'm not sure what that paper has to do with our current discussion, since it's about geneticists attempting to restore genetic function (protein production) via gene therapy. IOW, it's not really about natural DNA repair, and is instead about people trying to find ways to fix broken genes through our own intervention.

But, I don't want to unnecessarily bog this discussion down, so if you'd rather continue presenting your scenario, I'm fine with that.

If you want an example of an error that resulted in a mutation, which did not hamper functionality of the affected gene, you will have to give me a day or two. Meanwhile, see if this helps.
The Human CSB (ERCC6 ) Gene Corrects the Transcription-Coupled Repair Defect in the CHO Cell Mutant UV61

 

[Jose Fly]

If you want an example of an error that resulted in a mutation, which did not hamper functionality of the affected gene, you will have to give me a day or two.

No, that's ok. We covered that already (when we discussed functional redundancy).

Meanwhile, see if this helps.
The Human CSB (ERCC6 ) Gene Corrects the Transcription-Coupled Repair Defect in the CHO Cell Mutant UV61

Thanks! That paper does contain some info that may be helpful as we continue with your scenario.

 

[Hockeycowboy]

Confusingly false.



Look in the outhouse. Your paper comes in perforated rolls, or a SEARS book from the last century.

Don’t be abusive and sarcastic.

Actually, the telomere description is accurate...look it up.

 

[nPeace]

No, that's ok. We covered that already (when we discussed functional redundancy).


Thanks! That paper does contain some info that may be helpful as we continue with your scenario.

Okay, good. I'll conclude tomorrow.

 

[Jose Fly]

Okay, good. I'll conclude tomorrow.

Sounds good!

 

[dad]

That’s a reasonable assumption, with which I agree!

We have no idea how perfect DNA would appear.

It seems our telomeres, on the ends of our chromosomes, get shorter with age. (Maybe that has some effect?)
Now, what if these telomeres didn’t get shorter, but always kept their length?

There is a paper on just such a study...can’t remember where I read it. It might be online.

In this day and age we may see telomeres doing stuff. The reasons that genetics work as it now does is because the atoms and cells and etc all behave a certain way. The reason they all exist and react and behave as they do is because of the laws and forces that exist that determine how atoms work. If nature was not the same, then a different nature would result in genetics conforming to that different nature. Our present genetics conforms to this nature.

 

[dad]

So how do we verify that a person travelled to the future?

You don't. How do we know anything?

 

[dad]

You're going to have to demonstrate that some god exists first, before we start attributing actions to it.

No. You don't get to invoke an imaginary godless past just because of some attitude problem that needs adjusting.

 

[Hockeycowboy]

@shunyadragon ,

Here’s the paper....

Telomere shortening and ageing. - PubMed - NCBI

 

[dad]

When and where do we see "spirits as rulers or influencing ancient history?"
Perhaps people dismiss it because there is no good evidence of such things. Have you presented any?

One example is that ancient Egypt records cite spirit gods/beings as the first rulers.