Another poor response to ERV evidence for common ancestry by a creationist.

[Naraoia]

Reply to Naraoia...
“As far as I can tell, Alu elements are copied pieces of host DNA that hijack other retrotransposons' machinery to jump. Nothing to do with viruses, endogenous or otherwise.”
I think you win this point. I can’t locate where I dredged up this one.

I guess we can now both say that we learned something from the ERV debate

My Null hypothesis would not include common decent but creationism.

My point is that the null hypothesis in that quote you posted also didn't include common descent. They start from imagining independent retroviral insertions, and explain why this is exceedingly unlikely to produce ERVs in orthologous positions.

 

[Zaius137]

“No, they use an effective population size of 10,000. This does not mean that the actual population size is 10,000. Rather, this is the population size once inbreeding and temporal variation are considered. The effective population size will always be smaller than the actual population size for most models (if I understand it correctly, sfs can correct me if I am wrong).”

You need to show me how to reduce a population of 4 million to a population of 10 thousand effectively. Correct me if I am wrong but aren’t some of these reductions based on Domesticated animals and populations teetering on extinction. . I must emphasize the article talked about ERV-K in recent human populations and even happening “today”.

Small populations are problematic, restricted populations have less of a gene pool to draw from. Teetering on the brink of extinction from disease or starvation are just further problems of small interbreeding populations.

There is no evidence for small populations over long periods of time outside the evolution paradigm (which needs it).

“Many scientists have stated that scientific theories must be based upon repeatable observations subject to testing, and be "falsifiable," so observations can refute the theory. “ Direct observations of recent human populations are evidence that it is farfetched.

I would say that these small populations over millions of years have there own problems and need empirical evidence.


“Insertional polymorphisms of endog... [AIDS Res Hum Retroviruses. 2004] - PubMed - NCBI”

Is this a ERV or a control gene gone amuck? I don’t think anyone can answer this question definitively at this time.

“Alu's move within the genome all on their own. ERV's are from exogenous sources which are retroviruses.”

No actually they require the exogenous help from the replication mechanism.

 

[Zaius137]

By Loudmouth...

Originally Posted by Zaius137 http://www.christianforums.com/t7567545-post59042591/#post59042591
“Remine ignores the effects of neutral substitutions that are linked to beneficial mutations. The closer a neutral substitution is to a beneficial mutation the higher the chance that the neutral mutation will hitchhike along with the beneficial mutation.”

“Then show why it is wrong”.

First line of the paragraph “ReMine ignores the effects of neutral substitutions that are linked to beneficial mutations.” If a neutral substitution is neutral it is not beneficial… mutually exclusive.

 

[cupid dave]

Nevertheless, these poor respomses from creationists ignors the major error in thier propagatioin of pre 19th century theology that was sourced in medieval insights both from science and religion.

 

[Huram Abi]

Your responses aren't any more reasonable or accurate than creationists, Cupid.

At least creationists don't try to alter the bible to suit the secular understanding.

 

[Naraoia]

Small populations are problematic, restricted populations have less of a gene pool to draw from. Teetering on the brink of extinction from disease or starvation are just further problems of small interbreeding populations.

There is no evidence for small populations over long periods of time outside the evolution paradigm (which needs it).

Loudmouth was not talking about small populations. EFFECTIVE population size is not the same as actual population size. The simplest way to put the difference is: not everyone gets to reproduce. (And of those who do, some may reproduce with close relatives.)

The online materials for Ridley's Evolution said it quite nicely:

In an ecological sense, the size of a population can be measured by simply counting the number of adults in a locality. However, for the theory of population genetics what matters is the chance that two copies of a gene will be sampled as the next generation is produced, and this is affected by the breeding structure of the population.

 

[Loudmouth]

You need to show me how to reduce a population of 4 million to a population of 10 thousand effectively.

I already gave you three references that do just that. The effective population size is an ideal population that represents all of the genetic diversity of the population being studied. For the modern human 5 billion person population the effective population size is only around 10,000. Let me repeat that. For the modern human 5 billion person population the effective population size is only around 10,000. It would only take 10,000 people to effectively represent the genetic diversity of modern humans. The effective population size removes the genetic redundancy of the larger population. To use an analogy, it is like simplifying the fraction 5/10 to 1/2.

I must emphasize the article talked about ERV-K in recent human populations and even happening “today”.

One of the papers does talk about HERV-K113 which is a full length ERV (i.e. it contains all of the viral genes) without any apparent mutations. The authors suggested that this retrovirus could be capable of becoming active again and reinfecting humans.

Small populations are problematic, restricted populations have less of a gene pool to draw from.

The diversity of the effective population is the same as the actual population. That's the whole point.

There is no evidence for small populations over long periods of time outside the evolution paradigm (which needs it).

I already gave you two papers that calculated the human effective population size. The effective population size used in the paper modeling HERV-K fixation is in line with the findings of other authors as found in peer reviewed papers.

“Many scientists have stated that scientific theories must be based upon repeatable observations subject to testing, and be "falsifiable," so observations can refute the theory. “ Direct observations of recent human populations are evidence that it is farfetched.

Which observations?

Is this a ERV or a control gene gone amuck? I don’t think anyone can answer this question definitively at this time.

I can answer it definitively, and I will cite the same paper I have cited several times in this thread.

Human Endogenous Retroviruses are expected to be the remnants of ancestral infections of primates by active retroviruses that have thereafter been transmitted in a Mendelian fashion. Here, we derived in silico the sequence of the putative ancestral “progenitor” element of one of the most recently amplified family—the HERV-K family—and constructed it. This element, Phoenix, produces viral particles that disclose all of the structural and functional properties of a bona-fide retrovirus, can infect mammalian, including human, cells, and integrate with the exact signature of the presently found endogenous HERV-K progeny.
http://genome.cshlp.org/content/early/2006/10/31/gr.5565706.short
​

When a consensus sequence is used to reconstruct the HERV-K sequences it produces a viable, infective retrovirus that has the same insertion patterns as seen in human HERV-K insertions. ERV's are the result of retroviral insertion.

As to you question of control genes, those are part of the viral genome. The Long Tandem Repeats (LTR's) that sit on both sides of the viral genome are very strong transcription promoters. They are used by the virus to hijack the host transcription machinery and produce new viral particles. To answer your question, yes they are "control genes". More specifically, they are VIRAL control genes.

No actually they require the exogenous help from the replication mechanism.

Exogenous means from outside of the cell, not from within. Alu's do not have an exogenous source. Alu's are mobile elements meaning that they hop around in the genome. ERV's do not, outside of recombination events.

 

[Loudmouth]

If a neutral substitution is neutral it is not beneficial… mutually exclusive.

"Genetic hitchhiking is the process by which an allele may increase in frequency by virtue of being linked to a gene that is positively selected.[1] Proximity on a chromosome may allow genes to be dragged along with a selective sweep experienced by an advantageous gene nearby. More generally, genetic hitchhiking can refer to changes in an allele's frequency due to any form of selection operating upon linked genes, including background selection against deleterious mutations."
Genetic hitchhiking - Wikipedia, the free encyclopedia

The closer a neutral mutation is to a beneficial mutation within a chromosome the less likely the mutations will be split up during meiosis. That is how neutral mutations can experience positive selection due to a nearby positive mutation.

 

[Zaius137]

Loudmouth...

“I already gave you three references that do just that. The effective population size is an ideal population that represents all of the genetic diversity of the population being studied”.

I think we were talking about the cost of fixation and neutral selection not genetic diversity in a population. Apples and oranges.

“One of the papers does talk about HERV-K113 which is a full length ERV (i.e. it contains all of the viral genes) without any apparent mutations. The authors suggested that this retrovirus could be capable of becoming active again and reinfecting humans.”

Paleovirology nonsense. These may turn out to be regulatory sequences.

“I already gave you two papers that calculated the human effective population size. The effective population size used in the paper modeling HERV-K fixation is in line with the findings of other authors as found in peer reviewed papers.”

Fixation parameters need to take into account the number of individuals in that population. The authors of this article interrupted the figure from evolution dogma and I use the actual estimated population from real numbers of human population in modern times. My problem with these papers in a nutshell.

By the way here is another example of the right hand not knowing what the left hand does in evolution… From a recent article in Oxford Journals.

“Including coding and noncoding sites, we estimate that the genomic deleterious mutation rate U = 4.2. The mutational load predicted under a multiplicative model is therefore about 99% in hominids.”

http://mbe.oxfordjournals.org/content/27/1/177.full

This estimate is for humans and would imply a birth rate of “B=2e^4.2” about 133 offspring per parent just to keep the small human population from going into extinction. Evolutionists are nuts…

 

[Zaius137]

“Remine ignores the effects of neutral substitutions that are linked to beneficial mutations. The closer a neutral substitution is to a beneficial mutation the higher the chance that the neutral mutation will hitchhike along with the beneficial mutation.”

OK so where exactly does ReMine neglect Genetic hitchhiking?

 

[Zaius137]

"Loudmouth was not talking about small populations. EFFECTIVE population size is not the same as actual population size. The simplest way to put the difference is: not everyone gets to reproduce. (And of those who do, some may reproduce with close relatives.)"

Let’s see 10,000 can reproduce so 4,000,000 – 10,000 leaves 3,990,000 eunuchs.

 

[Jazer]

For the modern human 5 billion person population the effective population size is only around 10,000. Let me repeat that. For the modern human 5 billion person population the effective population size is only around 10,000.

So around 4,000 years ago the worlds population could have been 10,000 people? I know in my family we have multiplyed from 2 people to about 12 million people in 600 years. That is 12 million decendants from a 50 year old women on her second marriage. Also she was a Plantagenet and there is no telling how many decendants there are today from the Plantagenet line of Kings in England.

Kings usually got to be a king because they could fight a war and that means they had land, food and lots of wives and children. So the world is filled with people of royal blood because they could feed and sometimes even educate their kids.

 

[USincognito]

So around 4,000 years ago the worlds population could have been 10,000 people?

No. And we don't even need genetic studies to know that. Archaeology shows us there was more than 10,000 people in 2000 BCE.

 

[Zaius137]

I am literal in Bible interpretation. I believe that all the worlds’ population came from the descendents from Noah. The calculation is simple and used today for all kinds of calculations concerning wild populations.

http://jewsandjoes.com/exponential-human-population-growth-from-noah.html

My point in using the secular human population from the Wiki is that evolutionists can not even maintain an argument against their own empirical evidence. Science does show the simplest explanation (consistent with Occam’s razor) is the Biblical story of the origin of human population. That is another post all together; let us carry on with the current evolution problem of evidence for common ancestry.

 

[Mike Elphick]

I am literal in Bible interpretation. I believe that all the worlds’ population came from the descendents from Noah. The calculation is simple and used today for all kinds of calculations concerning wild populations.

Exponential Human Population Growth from Noah

My point in using the secular human population from the Wiki is that evolutionists can not even maintain an argument against their own empirical evidence. Science does show the simplest explanation (consistent with Occam’s razor) is the Biblical story of the origin of human population. That is another post all together; let us carry on with the current evolution problem of evidence for common ancestry.

This is nonsense, but first let's investigate your link, which is not a wiki, nor is it secular. At the top of the article is a graph depicting exponential growth:-

where (No) represents the initial population. (r) represents the natural growth rate, which factors in both birth and death rates. (t) represents the amount of time... using the same units as (r). (e) represents the base of the natural logarithms (approximately 2.71828). (N) represents the final resultant population. Plotted on a graph, the equation would look like the green curve in the image (assuming a natural growth rate of more than .01 or 1%).

There follows a link to a FoxNews article which describes the theoretical work in human population growth by Steve Olson and colleagues Statisticians: Common Ancestor of All Humans Lived 5,000 Years Ago

The jewsandjoes article then goes on to state:-.

Exponential population growth is a fundamental component in the computer simulation of the news story above. It is difficult for most people to fathom today's world population reaching it's current number in less than 5,000 years, but when the phenomenon of exponents is considered properly, it doesn't take any great mental leap.

However, Olson et al do not use such a simplistic equation, as implied. In his colleague's paper in Advances in Applied Probability "Recent Common Ancestors of all Present-Day Individuals" Joe Chang describes the mathematical models and they are clearly completely different and the word "exponential" is not even mentioned!

Conclusion: the jewsandjoes, article is deceiving its readers and cannot be used to support the biblical story of the origin of the human population and its subsequent growth.

But this is no surprise. No population of any organism can grow exponentially indefinitely. Just consider bacterial growth: they can double their population size in minutes, so why isn't the Earth covered with slime, or overrun by rabbits? The reason is that population growth is limited by the carrying capacity of the environment.

For some people, human beings seem to be the only creatures on Earth!

 

[Zaius137]

“This is nonsense, but first let's investigate your link, which is not a wiki, nor is it secular. At the top of the article is a graph depicting exponential growth:-“

The Wiki contained my value for estimated population. The cited article contained the argument for the population that we see today.

Actually if you look at the graph of the Wiki article you see that base population of humanity about 2000 years ago was estimated at 4 million. If I read it right.

I skimmed the paper you cited… it uses the same old evolution assumptions.

1) Wright-Fisher model for populations.
2) MRCA from a mitochondrial Eve of 100,000 to 200,000 years.

These same evolution assumptions return to a common ancestor from chimp and human of that unrealistic deleterious mutation estimation of (U=4.2). You really need to respond to that…


Are you claming that you cannot use the exponential calculation for population? Population calculations of all kinds of wild populations use this very calculation for an estimating future and past population values. The “k” value incorporates the of observed growth rates in the past of a population. What is wrong with using the actual observed rates…. The answer is simple; it does not fit the evolutionary assumptions.

I notice that Homo erectus is mentioned in this article as an ancestor of Humans of about 1.6 million years ago. Great until they discovered Turkana Boy which shows a human individual from that date. Isn’t it inconvenient finding a humanoid dated (by their standard) to 1.6-2.0 million years ago. Hey wasn’t that the beginning of the time that the human brain cavity was supposed to have expanded from 440 cc to about 1000 cc.

http://creation.com/turkana-boy-getting-past-the-propaganda

 

[Naraoia]

Are you claming that you cannot use the exponential calculation for population? Population calculations of all kinds of wild populations use this very calculation for an estimating future and past population values.

Umm, I'm going to need some citations for that. Back when I was taught ecology, we learned that population growth is commonly modelled by logistic equations. These take carrying capacity into account.

I notice that Homo erectus is mentioned in this article as an ancestor of Humans of about 1.6 million years ago. Great until they discovered Turkana Boy which shows a human individual from that date. Isn’t it inconvenient finding a humanoid dated (by their standard) to 1.6-2.0 million years ago. Hey wasn’t that the beginning of the time that the human brain cavity was supposed to have expanded from 440 cc to about 1000 cc.

Turkana Boy is an erectus/ergaster. (That distinction is largely a matter of where you stand on the lumper-splitter scale.) What's the problem?

 

[sfs]

“Including coding and noncoding sites, we estimate that the genomic deleterious mutation rate U = 4.2. The mutational load predicted under a multiplicative model is therefore about 99% in hominids.”

http://mbe.oxfordjournals.org/content/27/1/177.full

This estimate is for humans and would imply a birth rate of “B=2e^4.2” about 133 offspring per parent just to keep the small human population from going into extinction. Evolutionists are nuts…

No, 133 offspring is the number that would be needed for every generation to have genetically flawless individuals in it. This is clearly not the case for humans, or for any other complex organism.

 

[sfs]

“Remine ignores the effects of neutral substitutions that are linked to beneficial mutations. The closer a neutral substitution is to a beneficial mutation the higher the chance that the neutral mutation will hitchhike along with the beneficial mutation.”

OK so where exactly does ReMine neglect Genetic hitchhiking?

Where in the scientific literature has ReMine ever presented a calculation of anything? If you think he's able to calculate a stringent limit on the number of neutral substitutions that can take place in a species, present it.

 

[Mike Elphick]

This is nonsense, but first let's investigate your link, which is not a wiki, nor is it secular. At the top of the article is a graph depicting exponential growth:-

The Wiki contained my value for estimated population. The cited article contained the argument for the population that we see today.

The article you cited (from jewsandjoes.com) presents a population graph and equation implying that these were used as the basis for human population growth as estimated by Steve Olson and colleagues in the linked-to article from FoxNews. That, however, is a deception because Olson and Chang never used such an equation, as I very clearly demonstrated. In fact it is obvious they could not use such an equation.

Actually if you look at the graph of the Wiki article you see that base population of humanity about 2000 years ago was estimated at 4 million. If I read it right.

You are wrong! The two axes are simply labelled X and Y, time and population size, but they lack any units. It looks like the graph was simply knocked together by jewsandjoes in their attempt to deceive its readers. (Actually, I've just discovered it was lifted from here, where it is presented as an example of different types of growth).

I skimmed the paper you cited… it uses the same old evolution assumptions.

1) Wright-Fisher model for populations.
2) MRCA from a mitochondrial Eve of 100,000 to 200,000 years.

Well, I'm shocked, because the paper I quoted was used as the basis for the FoxNews article!

Seven years ago one of Olson's colleagues, a Yale University statistician named Joseph Chang, started thinking about how to estimate when the last common ancestor of everybody on Earth today lived.

In a paper published by the journal "Advances in Applied Probability," Chang showed that there is a mathematical relationship between the size of a population and the number of generations back to a common ancestor.
FoxNews:- Statisticians: Common Ancestor of All Humans Lived 5,000 Years Ago

Do less skimming is my advice.

These same evolution assumptions return to a common ancestor from chimp and human of that unrealistic deleterious mutation estimation of (U=4.2). You really need to respond to that…

Eh? I'm dealing with the matter of how easily creationists can be misled by a graph combined with an unrelated news article.

Are you claming that you cannot use the exponential calculation for population? Population calculations of all kinds of wild populations use this very calculation for an estimating future and past population values.

As I said, no population can grow at an exponential rate indefinitely, though it can for a short period. Get wise and read this:- Principles of Population Growth

The “k” value incorporates the of observed growth rates in the past of a population. What is wrong with using the actual observed rates…. The answer is simple; it does not fit the evolutionary assumptions.

Here's a graph of the global human population since 10,000 BC. What do you think is wrong with it?