Mitchondrial DNA

[gluadys]

I also have a big problem with unassisted abiogenesis

God Bless
Jim Larmore

I should hope so. What about unassisted gravity? I trust you don't believe gravity works without God either.

 

[Mallon]

Here's some must-reading for those who would twist the meaning of Mitochondrial Eve to suit their neocreationist agenda:

http://www.talkorigins.org/faqs/homs/mitoeve.html
http://www.talkorigins.org/indexcc/CB/CB621.html

 

[Jimlarmore]

Not only does genetics powerfully support evolution; evolution is defined as genetic change.

Remember that evolution is a change in the distribution of alleles over generations. "Alleles" is a genetic term.

Tracing the pathways of evolution is a matter of tracing genetic change, either directly through DNA sampling, or indirectly through changes in morphology.

Mutations in and of themselves is not a viable modality to support new information in the genome. Look here to see:

http://www.phy.ornl.gov/csep/CSEP/MU/NODE8.html#SECTION00026000000000000000

It's basically like asking a train wreck to produce a better transportation system. 97% of all mutations are either harmful or at best neutral. Probability and statistics show this is not the cause of new information in the genome.

God Bless
Jim Larmore

 

[Jimlarmore]

I should hope so. What about unassisted gravity? I trust you don't believe gravity works without God either.

Can you explain how gravity works? I'd love to hear your explanation.

God bless
Jim Larmore

p.s. on an edit:

I think it's necessary to explain that to my way of thinking now that I am no longer agnostic is this: Logically, the study of science does not have to show a natural first cause to explain a phenomenon. God's ability is beyond nature as we know it. Fiat creation in and of itself prooves this.

 

[Jimlarmore]

In terms of questioning the mainstream paradigm, I think the example is not exactly God on Mt. Sinai writing on stone, but a pretty unlikely match between the stories of Adam/Eve and Noah. While not overwhelming in content, the scoffers should take this opportunity to admire in silence and give credit where its due. Funny how the Bible always seems to be right.

For the record I am not saying the mitochondrial Eve was the Eve in Genesis. We know from the limited information in the mitochondria and the nucleus that there was an extreme necking down of the genome a few thousand years ago. This could very well co-incide with the global flood event of Noah time.

God Bless
Jim Larmore

 

[Jimlarmore]

Also to clarify what I meant by the mutations on the "Y" chromosome. I did not mean there were no mutations at all on the "Y" chromosome. Only the segment that makes a male a male. If mutations did occurr on this segment phenotypically the offspring could not contribute this to the gene pool.

God Bless
Jim Larmore

 

[juvenissun]

Do I care? No.

Tell you what. Work with the OP and find something good in it. It is proof that you are really engaged on the issue. Anyone can find a reason to attack relentlessly on any position. Once you take the other approach, there will be a basis to proceed.

Then I will care.

I argue and fight with people for a living. I am more than able here, but would prefer not to.

Interesting. Well said.

 

[sfs]

Also to clarify what I meant by the mutations on the "Y" chromosome. I did not mean there were no mutations at all on the "Y" chromosome. Only the segment that makes a male a male. If mutations did occurr on this segment phenotypically the offspring could not contribute this to the gene pool.

God Bless
Jim Larmore

You're presumably talking about the SRY gene. There are no known mutations that change the protein produced by the gene, but there is one known variant within the gene; it is a synonymous substitution, i.e. it codes for the same amino acid as the original. It's officially known as rs11575897, should anyone want to look it up in dbSNP or in a genome browser.

 

[juvenissun]

Mutations in and of themselves is not a viable modality to support new information in the genome. Look here to see:

http://www.phy.ornl.gov/csep/CSEP/MU/NODE8.html#SECTION00026000000000000000

It's basically like asking a train wreck to produce a better transportation system. 97% of all mutations are either harmful or at best neutral. Probability and statistics show this is not the cause of new information in the genome.

God Bless
Jim Larmore

But, how about the rest 3%? If a long time is given, the 3% figure could become significant.

I guess not. 3% of 3% of 3% of ... Would it become nothing in a short period of time?

 

[juvenissun]

You're presumably talking about the SRY gene. There are no known mutations that change the protein produced by the gene, but there is one known variant within the gene; it is a synonymous substitution, i.e. it codes for the same amino acid as the original. It's officially known as rs11575897, should anyone want to look it up in dbSNP or in a genome browser.

So, what could be the consequence of that variant?

 

[gluadys]

So, what could be the consequence of that variant?

None. That is why it is called synonymous. The variant produces the same amino acid and therefore the gene produces the same protein product as if there were no difference in the DNA.

It is rather like one of those small spelling differences between British and American English. "honour" vs. "honor". Both words sound the same and mean the same.

 

[gluadys]

Mutations in and of themselves is not a viable modality to support new information in the genome.

So what? Since when is evolution about new information?

And how do you define and measure genetic information, anyway?

Can you show me any definition of genetic information that makes evolution not possible?

97% of all mutations are either harmful or at best neutral.

Again, so what? How does this stand in the way of evolution?

btw, there is one error in the linked page.

If a mutation occurs in a recessive gene it may not be expressed, i.e. the effects of the mutation will not be seen. In these cases the mutation is carried in the genes of the individual, and may be passed on to successive generations, only to show up as a harmful mutation in a later generation when an individual with homozygous recessive genes is produced.​

A mutation in a recessive gene is not necessarily harmful. As with mutations in dominant genes, it may be beneficial or neutral. So when it shows up in an individual with homozygous recessive genes, the effect will not necessarily be harmful. I expect the ratios for mutations in recessive genes are the same as in dominant genes i.e. 97% are neutral or harmful.

 

[gluadys]

Can you explain how gravity works? I'd love to hear your explanation.

God bless
Jim Larmore

As far as I know, no one has a handle on how gravity works. However, we do know that it does work, that we can measure its effect and formulate an equation that accurately predicts gravitational effects in all but quantum level events.

Do you think it works without divine assistance?

btw, can you explain how evolution works? Or at least how scientists say it works. I am not asking that you believe the scenario biologists set out. Just wondering how familiar you are with it.

 

[Jimlarmore]

So what? Since when is evolution about new information?

And how do you define and measure genetic information, anyway?

Can you show me any definition of genetic information that makes evolution not possible?

Absolutely, biochemistry tells us it's impossible on so many different levels but lets examine just one that you don't hear about too much and that is genetic differences.

Techniques exist today to measure the degrees of similarity between forms of life on the chemicals of life level. These genetic differences are calculated by taking a specific protein and examining the sequences of it's amino acids. The fewer changes needed to convert a protein of one oganism into the corresponding protein of another organism, supposedly the closer their relationship. Similar comparisons can also be made between the DNA and RNA of different organisms. Guess what most species exist in isolation and there isn't close similarities. There is not a single shred of evidence for the traditional way science says evolution to happen the way it did. There has been huge investments in research on this. The lastest using a computer-based study on "cytochrome c" where 47 different forms of life were compared. For evolution to be valid the study should have shown similarity in say snakes with other reptiles but guess what again. A rattle snake was closer to man than other reptiles .

A mutation in a recessive gene is not necessarily harmful. As with mutations in dominant genes, it may be beneficial or neutral. So when it shows up in an individual with homozygous recessive genes, the effect will not necessarily be harmful. I expect the ratios for mutations in recessive genes are the same as in dominant genes i.e. 97% are neutral or harmful.

The drosopila ( fruit fly ) has been mutated more than any other eukayote organism to date. Not one mutation has shown to increase the genomes information or cause the organism to be anything other than a fruit fly. Mutations are not a good modality for change like the evolutionary model suggests must take place.

God Bless
Jim Larmore

 

[Jimlarmore]

As far as I know, no one has a handle on how gravity works. However, we do know that it does work, that we can measure its effect and formulate an equation that accurately predicts gravitational effects in all but quantum level events.

Do you think it works without divine assistance?

I think God most likely created natural laws that function on their own to a great extent.

btw, can you explain how evolution works? Or at least how scientists say it works. I am not asking that you believe the scenario biologists set out. Just wondering how familiar you are with it.

Are you wanting me to speak on cladistics or supposed taxonomic changes? Or are you wanting to stay on the biochemical level?

God bless
Jim Larmore

 

[gluadys]

I think God most likely created natural laws that function on their own to a great extent.

So is it your contention that as long as nature is working as expected, God is absent?

Does God only show up when nature is incapable of doing what God wants done?

Are you wanting me to speak on cladistics or supposed taxonomic changes? Or are you wanting to stay on the biochemical level?

Neither. Start with population genetics.

There has been huge investments in research on this. The lastest using a computer-based study on "cytochrome c" where 47 different forms of life were compared. For evolution to be valid the study should have shown similarity in say snakes with other reptiles but guess what again. A rattle snake was closer to man than other reptiles .

Actually, it was a high-school science fair project.

Brown claimed that on the basis of data from a 1978 study by Margaret Dayhoff, comparisons of cytochrome c show that the rattlesnake is more closely related to humans that to any other organism. When [Robert] Kenney asked Brown to provide the name of the scientific journal and the page number in which Dayhoff had reached this conclusion, Brown stated that he couldn't. Dayhoff had never reached such a conclusion, but rather Brown’s son had used Dayhoff’s data to reach that conclusion for a science fair project. It was Brown’s son who had concluded that rattlesnakes are more closely related to humans by cytochrome c than to any other organism.

For fifteen dollars, Brown sent Kenney photocopies of his son’s project (apparently, Brown’s price depends on who you are). Kenney wrote:

“In the project I quickly found that the rattlesnake and humans differed by only fourteen amino acids. Humans and rhesus monkeys differed by one amino acid. Later, Brown called me again and then explained that of the forty-seven organisms in the study, the one closest to the RATTLESNAKE was the human, not that the one closest to the human was the rattlesnake. You see, among the forty-seven there were no other snakes.” (CEN Vol.4 No.5 Sep/Oct 84, pg 16)

Most of the other organisms in the study were as distantly related to the rattlesnake as were humans; it is coincidence that human cytochrome c was just barely less different than the others.​

Emphasis added

http://members.cox.net/ardipithecus/evol/lies/lie025.html

The drosopila ( fruit fly ) has been mutated more than any other eukayote organism to date. Not one mutation has shown to increase the genomes information or cause the organism to be anything other than a fruit fly.

Why, on the basis of the theory of evolution, would you expect it to be anything other than a fruit fly?

Also, none of this contradicts my point that a mutation in a recessive gene is neither more nor less likely to be harmful than a mutation in a dominant gene.

 

[Jimlarmore]

So is it your contention that as long as nature is working as expected, God is absent?

Does God only show up when nature is incapable of doing what God wants done?

Do you believe in God? If so then what do you feel His role in the universe is?

Neither. Start with population genetics.

Well, I'm not going to jump thru a bunch of hoops just to satisfy your little fancy so let's focus on one or two areas. The modern evolutionary synthesis has a lot to say on mathematical population genetics. Then there is a lot on genetic drift, mutations or gene/allele flow. So where do you want to go with this? BTW, how would I know if you even knew what you were talking about or not?


Walt Brown's son's work may not be that far off. Look at this:

http://www.windsorpark.org.nz/Feature/Cytochrome divergence.asp

Why, on the basis of the theory of evolution, would you expect it to be anything other than a fruit fly?

Also, none of this contradicts my point that a mutation in a recessive gene is neither more nor less likely to be harmful than a mutation in a dominant gene.

Your statement concerning a mutation in a recessive or dominant gene is vague because it is a blanket statment and cannot apply to all mutations of recessive alleles. If a mutation occurrs on a dominant gene or recessive gene it can cause diseases such as Tay Sachs disease
http://en.wikipedia.org/wiki/GM2_gangliosidosis

or this; http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Mutations.html

or this:
http://genetic-diseases.net/

Getting back to drosophila. The modality given for change in the biota is mutations yet in over 70 plus years and tens of thousands mutations later we still don't see anything but detrimental changes to this animal and no new genomic information as a result. Mutations have not been shown to be a good causitive agent for the diversity in the biota.

God Bless
Jim Larmore

 

[juvenissun]

The drosopila ( fruit fly ) has been mutated more than any other eukayote organism to date. Not one mutation has shown to increase the genomes information or cause the organism to be anything other than a fruit fly. Mutations are not a good modality for change like the evolutionary model suggests must take place.

I heard that same fruit flies fed by different food and "evolved" into two groups that do not mix breed. Is this relevant to what you said?

 

[juvenissun]

I think God most likely created natural laws that function on their own to a great extent.



Are you wanting me to speak on cladistics or supposed taxonomic changes? Or are you wanting to stay on the biochemical level?

God bless
Jim Larmore

Stay on the biochemical level. Please.

 

[sfs]

When it comes to DNA humans have more than just nuclear DNA. In the cell's energy producers called mitochondria there are strands of DNA that came only from our mothers. So all mitochondrial DNA comes only from the female side of the union that produces an offspring.

A probing question of course should be where did the first female get her mitochondrial DNA? Likewise the "Y"chromosome that determines whether an embryo will be male or not comes only from the Father.

This is all correct.

Focusing however on the female side of this science has found that all humans have the same mitochondrial DNA. This conclusion came in 1987 by a team from the University of California at Berkely who published a study comparing the mtDNA of 147 people from five of the worlds geographical locations. They concluded that all 147 had the same female ancestor later dubbed her "Mitochondrial Eve".

This is pretty garbled. Humans do not all have the same mitochondrial DNA (mtDNA); our mtDNA all derives from a single female, but it has mutated along the way, so it differs from person to person. And the point of the study was not to establish that there was a single ancestor of all mtDNA, because everyone already knew that. Every bit of our DNA has a single common ancestor somewhere in the past -- that's an inevitable consequence of population genetics for a finite population size. The point was to estimate when and where the common ancestor lived.

To me I would be seriously interested in finding out how long ago this woman lived. The shocking discovery based on the frequency of mutations that occurr on the mtDNA we can conclude that Mitochondrial Eve lived approxiamately 6,000 to 6500 years ago. ( Ann Gibbons, "Calibrating the Mitochondrial Clock" Science, Vol 279, 2 Jan 1998 p. 29 ).

Well, you can conclude that mtDNA Eve lived 6000 years ago only if you ignore the article you're citing. The article itself points out that to get an age of 6000 years you would have to use an obviously incorrect mutation rate. The point is that the mutation rate used in the original mtDNA Eve paper gave too large an age. The correct value lies somewhere in between, but it is not obvious yet exactly where.

Mitochondrial DNA, it turns out, is really quite a poor choice for trying to estimate genetic ages. There are at least two important effects. First, the mutation rate varies a lot from spot to spot in mtDNA. As a result, if you measure mutation rates over short periods of time (a few generations), you will find a high rate. If you look over longer periods of time, you will see more mutations, but not as many as you would expect from the mutation rate: the hotspots of mutation will have mutated many times, but multiple mutations in the same base do not accumulate. Second, a large fraction of mtDNA is functional, and so many mutations are somewhat deleterious. When you measure mutations over a few generations, you will see a lot of mutations that will end up being weeded out by natural selection.

The net effect of the two processes (and probably some others as well) is that mutation rates measured directly are much higher than the rate that mutations accumulate over millions of years. If you use the high value for the rate, you will get the 6000 year estimate for mtDNA Eve; if you use the low value, you will get 160,000 years.

There are couple of ways of handling the problem. One is to skip mtDNA entirely and use autosomal DNA, which is the vast bulk of the human genome, and which is much less problematic when it comes to estimating mutation rates. (This is because only a small fraction of the autosomal DNA is functional, and because the mutation rate is much, much lower in the autosomes, as well as less variable, than in mtDNA. Thus neither factor mentioned above has much impact.) For the autosomes, the mutation rate estimated from human/chimpanzee divergence agrees very well with the rate estimated from new mutations occurring today in humans. If you use the autosomes, you will find that the average time to the most recent common ancestor of those parts of DNA averages out to around 800,000 years. (Because of the different mode of inheritance, autosomal DNA is expected to have an age that is four times larger than mtDNA or the Y.)

Second, you can try to model the various effects on the mtDNA mutation rate and correct for them. There are studies doing just that (in fact one was published just this month in the American Journal of Human Genetics); they estimate ages for mtDNA Eve in the range 75,000 to 110,000 years ago.

The same thing exists in the "Genetic Adam" and the "Y" chromosome. From a world wide study of 38 men there appeared no difference in the "Y" chromosome at all. Had humans evolved and all men descended from one male who lived millions of years ago each should carry at least 40 or more mutations. No changes were found.

Where on earth did you get the idea that human Y chromosomes should date back millions of years? According to basic population genetics theory, the expected age (measured in generations) of the most recent common ancestor of chromosomes like the Y is equal to the size of the population (technically the effective population size). The effective population size for humans is about 10,000, so we would expect Y Adam to have lived roughly 10,000 generations ago, or about 200,000 years, with a large uncertainty (technically, the standard deviation on the age is also equal to 200,000 years). 100,000 years is quite plausible, but millions would be surprising.

It's also not true that human Y chromosomes are all the same. There are at least hundreds of genetic variants known on the Y. (Elsewhere you say that you're only talking about one gene on the Y, the one that causes males to develop as males (which is SRY), but that makes no sense. Even if the common ancestor of all Y chromosomes had lived millions of years ago, we would not expect to find 40 mutations in a single gene. Plus, there is a mutation known in SRY.)

Just a few things to question the mainstream paradigm.

You need to learn more about the science before you can question it effectively.