Pete's Quite Thread post

[gluadys]

I wanted to save this one for last. The mechanism is a fixed mutation in populations leading to the rise of a distictly different genus like humans.

Now you are confounding different levels of mechanism. The mechanism which changes a genome is mutation. Then there are mechanisms which cause mutations in the first place. A fixed mutation is a change in the genome which affects all or nearly all members of the species. But you also have to keep in mind the mechanisms which bring about fixation.

No one fixed mutation will ordinarily lead to speciation, much less give rise to a new genus. Not only do you need many mutations and many fixations, you also need a mechanism to divide the population into isolated groups.

So you can't pin anything down to one mechanism. You need to look at a variety of mechanisms of different kinds at different points in the process.

There is definately a process that must involve things changing at a nucleotide level, an amino acid sequence level, a protein level

Yes, and further at a morphological level and a gene pool level as well.

and none of these changes without signifigant, if not grave, risks.

And where are the significant, if not grave, risks felt? You have not demonstrated yet that the population is at risk.

Ok, so we are going to abandon the steps required for mutations to result in adaptive evolution and get right to the effects when expressed in the phenotype. That is begging the question a little is it not? Sure, it will be preserved if it gets to the point where there is a signifigant advantage but getting from point A to point B, C and D has many pitfalls and trappings that we can't ignore.

Don't be silly. I was not talking about abandoning any steps at all. I was talking about identifying the point at which one can speak of benefit.

If A is a change in an DNA sequence and B is a resulting change in an amino acid sequence, and C is a resulting change in a protein and D is a change in expressed morphology due to the change in the protein, when, in this sequence can we speak of a beneficial change? We can have no idea whether a change is beneficial, neutral or harmful until we get to D. And even then we need a measure of differential reproductive success to tell us whether it is beneficial. We can't tell just by looking at the change.

So to say that A (the mutation) is "beneficial" is really a retrospective judgment. We can't tell from A (or B or C) that the change is beneficial. All we can say is that we have evidence in the form of differential reproductive success that D is beneficial. If we can then identify A as the cause (via B and C) of D, we can identify A as beneficial.

We can look at the intensity of the overall effects of mutations by comparing a single base substitution to an indel, that much is certain.

And that too may vary. An indel affecting 100 base pairs may have a less intense overall effect than a single base substitution. We can't simply count base pairs to determine intensity of effect.

We know what happens most of the time when they are expressed in the phenotype, that is even clearer still. What is even more important, we know the limits of this kind of change in positivly benefiting populations by looking at their rare occurance in nature. A slight selective advantage for a small minority for a short time, couldn't be any clearer if you were looking at it under a microscope.

Again, you have to factor in environmental conditions. A short term change in annual rainfall levels that reverts to normal will give you the fluctuating changes in the beak of Galapagos finches. But a long-term climate change stretching over hundreds of thousands of years---like the Pleistocene ice age--will lead to long-term changes in a single direction. Similarly a permanent change in ecological niche--like moving from terrestrial habitat to marine habitat fosters permanent changes.

Funny you should mention that, it is the effect of the environment that I am most interested in. I won't go into the particulars right now but that is what I am browsing on the internet when I'm not talking to you guys.

Well keep it up. It may finally help develop some comprehension of natural selection.

Mutations is not a perfectly good word since a mutations are transcript errors

No, mutations are not transcript errors. Mutations are changes in DNA sequences. Copying error is a common mechanism which creates these changes. You are confusing the mechanism (copy error) with the result (mutation).

I am not on here trying to convince anyone of anything, I am trying to get to the part where we explore these mechanisms but it takes a lot of time.

You are right. It takes time because evolution is a complex process involving many mechanisms at many levels---some in the cell, some in individual organisms, some in populations. You have been fixated for some time on the first two. Changing focus to environmental factors may help you with the third.

 

[mark kennedy]

Glaudys, you are a peach, I'll get to your post tommorow after work.

Grace and peace,
Mark

 

[JesusQuest]

An encyclopedia at home said 99 percent of all mutations are defects. If after millions of years we have been defected why are we smarter and better than those single celled organisms science says we began as?

 

[Pete Harcoff]

An encyclopedia at home said 99 percent of all mutations are defects. If after millions of years we have been defected why are we smarter and better than those single celled organisms science says we began as?

Your encyclopedia is confusing you. In general, most mutations are neutral (probably 95% are more). A high proportion of the remaining mutations are deleterious, while a small fraction are beneficial.

The key in evolving populations is that deleterious mutations generally get weeded out of the population via natural selection, while beneficial mutations are preserved.

 

[gluadys]

An encyclopedia at home said 99 percent of all mutations are defects. If after millions of years we have been defected why are we smarter and better than those single celled organisms science says we began as?

To add to what Pete has said, it is important to remember that mutations happen to individuals while evolution happens to populations. So the question about mutations which cause defects is this: "Is the defect spreading into the population?"

Serious defects may cause an individual to die before reproducing, make it difficult to find a mate, make one sterile or one's offspring sterile or less likely to thrive. So they tend to show up rarely, and not invade the species gene pool to any extent.

A benefit, on the other hand, no matter how small, will tend to help an individual live through their reproductive span, acquire a mate easily and have healthy thriving children who will enjoy the same advantages and pass them on to their children. Depending on the size of the population, the new beneficial trait can spread to all the population in a few generations. So a beneficial mutation soon takes over the whole species gene pool.

 

[Manic Depressive Mouse]

Well it's good that Mark's admitted, as much as his arrogence allows, that he's talking garbage about humans not speciating.

 

[Loudmouth]

There is going to be a far more unlikely scenerio for creating a selective advantage then a deleterious one, that's for sure

Why?

The mechanisms I have seen and accept somewhat would be things like gene duplication and transposons. One of the major differences is in keeping the reading frame open but I think you can get the general idea of the differences I would expect.

Transposons and gene duplications are types of mutations. They occur randomly, that is without preference towards benefice, neutrality, or detriment.

One big difference, there is going to be a winner eventually in every state lottery, that's a given. When it comes to mutations (transcript errors as opposed to functional advantages) there is no such guaranteed winner and a lot of losers.

There is a guaranteed winner, the ancestor with the most grandchildren.

Yes, but what do you win, when you win and what is lost when you lose.

The winning are the overabundance of your genes in subsequent generations. When you lose, your genes are eliminated from the species gene pool. The winners and losers are determined by natural selection.

There are no lethal effects that result from a random quick pick at the local lottery ticket distributer, there are for random mutations.

Which would make natural selection a powerful tool indeed.

A slight selective advantage that has sever deleterious effects in a minority of the population. If the actual immunitiy systems were being improved they would have far reaching effects that would fix them in populations with advantages that far exceed resistance to malaria. This is not happening and its more of the same anecdotal evidence for evolution that is equivacated with adaptation ever time.

Hemoglobin C is not lethal or detremintal, even in heterozygotes. You are thinking of the sickle cell allele. HemC is a mutation of the HemS (ie sickle cell). HemC is a toned down version; it allows infection to occur but only mild infections result. Carriers of one or two copies of HemC have the same protection. Carriers of two copies have very, very mild side-effects, especially when compared to sickle cell. This is why HemC is poised to overrun HemS in African populations that are regularly exposed to malaria.

Well, unless you are suggesting that the single common ancestor was a human germcell I don't think you are comparing apples to apples here

No, I am suggesting that the single common ancestor was a single cell, just like you when you were a single diploid cell right after fertilization.

What is more it was not mutations that caused my genome to expand from hundreds/thousands of bps to millions of them.

That's what mutations do, add to the genetic material. Genome duplications have been observed and are considered to be mutations.

The DNA code was allready there in virtually every cell that was produced and mutations that effected my development most likely would have been deleterious if not lethal.

Evidence?

Apparently we have very different ideas on what constitutes a benefitial effect. Now for an improved immunity to malaria and other diseases to manifest itself I would be as excited as any evolutionists to see it. An inheritable trait that improves vital organs to the point of giving then a selective advantage could go so far as to convert me to died in the wool darwinism.

The circulatory system is not a vital organ? Has not HemC improved it? Why does increased immunity not qualify as a good example of evolution?

 

[mark kennedy]

There is going to be a far more unlikely scenerio for creating a selective advantage then a deleterious one, that's for sure

Why?

Basic biology, the DNA is translated and the RNA transcribed into a precise series of amino acids that fold into proteins and eventually are built into cells. It is far more likely that a random mutation will throw a monkey wrench into the works since the sequences are very precise, a single insertion can shut down the reading frame or produce a garbled protein.

To put it in perspective, I can find a list of diseases or disorders for every single chromosome in the human genome. The beneficial mutations are, on the other hand, rare in comparison, that's why LM.

Transposons and gene duplications are types of mutations. They occur randomly, that is without preference towards benefice, neutrality, or detriment.

Since I have nothing but a vauge suspicion that there is an actual mechanism for a cut and paste function in gene splicing and gene duplication I couldn't argue otherwise.

There is a guaranteed winner, the ancestor with the most grandchildren.

That is the circular element of survival of the fittest. Who are the fittest? Why, its the one who survive of course. Who is it that survives then? Why, its the fittest of course.

The winning are the overabundance of your genes in subsequent generations. When you lose, your genes are eliminated from the species gene pool. The winners and losers are determined by natural selection.

Then why is it that all mammals have around 24,000 genes on average dispite the fast differences in the expression in their perspective phenotypes?

Which would make natural selection a powerful tool indeed.

Natural selection is a metaphore based on artificial selection and the issue is the preservation of favorable traits. According to Darwinian dogma the favorable traits are fixed and continued as the result of the mass extinction of those who lack favorable traits. Would you agree or do you tend to favor genetic drift rather then traditional Darwinian concepts?

Hemoglobin C is not lethal or detremintal, even in heterozygotes. You are thinking of the sickle cell allele.

"The most important aspect of identifying people with Hemoglobin C trait is informing them of their risk of having a child with a serious disease."

http://www.vh.org/pediatric/patient/pediatrics/faq/hemoglobinc.html

HemC is a mutation of the HemS (ie sickle cell). HemC is a toned down version; it allows infection to occur but only mild infections result.

Hemoglobin C is a hemoglobinopathy, caused by an inherited abnormality of the beta globin gene. This disorder is inherited as an autosomal recessive trait. Hemoglobin C produces a mild type of anemia that occurs because the red blood cells containing abnormal hemoglobin are broken down prematurely.

Normal hemoglobin, known as hemoglobin A, is also present. The spleen may be enlarged, and there may be jaundice, a yellow color of the skin. Gallstones may develop and require treatment in adulthood.

The disease occurs predominantly in the black race. A family history of hemoglobin C is a risk factor. In combination with sickle hemoglobin, it results in Hemoglobin SC disease, which is characterized by hemolysis and painful crises. It is usually milder than sickle cell disease...A complication is gallbladder disease.

http://www.nlm.nih.gov/medlineplus/ency/article/000572.htm

Carriers of one or two copies of HemC have the same protection. Carriers of two copies have very, very mild side-effects, especially when compared to sickle cell. This is why HemC is poised to overrun HemS in African populations that are regularly exposed to malaria.

To the best of my knowledge this particular mutation results in an amino acid substitution producing a deformed blood cell. It does give a signifigant advantage but only in the resistance to malaria and there are very real side effects and it is a pathological disorder. However, this is an eye opening beneficial effect and typical of beneficial effects from mutations. It occurs in a small minority and offers only a slight advantage for a short time.

No, I am suggesting that the single common ancestor was a single cell, just like you when you were a single diploid cell right after fertilization.

I realize that and it's not a bad analogy but it is hardly the same thing. The actual molecular mechanisms are very different and my point was that recapitulation is not the same as a demonstrated mechanism.

That's what mutations do, add to the genetic material. Genome duplications have been observed and are considered to be mutations.

Evidence?

"Except for the eggs and sperm, each cell in the human body -- there are 100 trillion cells in each of us -- contains the entire human genome, all the genetic information necessary to build a human being, and this information is encoded within the cell nucleus in 6 billion base pairs, subunits of DNA, packaged in 23 pairs of chromosomes, one chromosome in each pair coming from each parent. "

http://www.medterms.com/script/main/art.asp?articlekey=8591

On the other hand the single celled common ancestor would not have been a sex cell and the genome would have been in the thousands of bps, not the millions required for eukaryotes.

The circulatory system is not a vital organ? Has not HemC improved it? Why does increased immunity not qualify as a good example of evolution?

There is ample reason to believe that it is beneficial in a small minority in limited circumstances but it is hardly adaptative evolution. The only way natural selection could fix this trait is for it to eliminate all of the less fit. The issue I raised with Pete and his post was the fixation of the tens of thousands of differences between chimps and humans, particularly in the effective genome.

Bottomline, a single amino acid substitution does not qualify as an adaptative evolution. Don't get me wrong, I enjoyed responding to this post and it was a refreshingly substantive argument.

 

[gluadys]

Basic biology, the DNA is translated and the RNA transcribed into a precise series of amino acids that fold into proteins and eventually are built into cells. It is far more likely that a random mutation will throw a monkey wrench into the works since the sequences are very precise, a single insertion can shut down the reading frame or produce a garbled protein.

To put it in perspective, I can find a list of diseases or disorders for every single chromosome in the human genome. The beneficial mutations are, on the other hand, rare in comparison, that's why LM.

But that is not why at all. This only explains why beneficial mutations are rarer than harmful mutations. It also says something about why we call certain mutations harmful--because they express as disease or disorders.

But you never go to the next step. What is the impact on the gene pool of the species? What relevance does an individuals' genetically-based disease have on the next generation? How does a species handle the intrusion of genetically-based diseases and disorders into its population? And how does that compare with the fate of beneficial changes? Or even neutral changes?

 

[mark kennedy]

But that is not why at all. This only explains why beneficial mutations are rarer than harmful mutations. It also says something about why we call certain mutations harmful--because they express as disease or disorders.

I never did quite understand why the concept of there being molecular mechanisms that change the effective genome and a transcript error is so hard to grasp. When has there ever been a substantive advantage to one of my spelling errors in my posts?

But you never go to the next step. What is the impact on the gene pool of the species? What relevance does an individuals' genetically-based disease have on the next generation? How does a species handle the intrusion of genetically-based diseases and disorders into its population? And how does that compare with the fate of beneficial changes? Or even neutral changes?

Over generations mutations are purged whether they have a slight advantage that results or not, this is simply how it works. The reason is that when they do happen in the effective genome disease and disorder are often, if not allways the result. Effective genomes are not slightly rearranged in the Darwinian version of natural history, they undergo major overhauls. Vital organs and genes that effect them cannot withstand the level of changes it would take for humans to have a common ancestor with the chimp.

Mutations are dangerous and destructive, if there are molecular mechanisms that can alter and improve the effective genome then I would love to know what they are.

 

[gluadys]

I never did quite understand why the concept of there being molecular mechanisms that change the effective genome and a transcript error is so hard to grasp. When has there ever been a substantive advantage to one of my spelling errors in my posts?

That is easy to grasp. But that only affects the genome of the individual in whom the mutation occurs. I am asking you about the effect on the population as a whole.

Over generations mutations are purged whether they have a slight advantage that results or not, this is simply how it works. The reason is that when they do happen in the effective genome disease and disorder are often, if not allways the result.

ok, you are beginning to make progress. Because the effect on the genome is negative, these deleterious mutations are purged.

Purged from what?

What is the result of this purging on the population?

And what is the purging mechanism?

Mutations are dangerous and destructive, if there are molecular mechanisms that can alter and improve the effective genome then I would love to know what they are.

There are no molecular mechanisms that improve the effective genome. Molecular mechanisms produce mutations. And that is all. Whether the mutation will be neutral, harmful or beneficial to the species is not decided at the level of the molecular mechanisms.