Why evolution doesnt matter.

[itinerant1]

Just FYI: The Pontifical Academy of Science has made available online its publication Scientific Insights into the Evolution of the Universe and of Life. Scroll down the page to Acta, under which you will see the links to pdf files at, “020 Scientific Insights into the Evolution of the Universe and of Life. Plenary Session, 31 October - 4 November 2008, Vatican City, 2009, pp. LXVII-622, ISBN 978-88-7761-097-3.”

This is a good online source about evolution, which includes a presentation on the Intelligent Design challenge to evolution theory. Enjoy!

 

[DAMIENTHEGREAT]

Are you actually serious? You believe in utter, unproved and poorly recorded nonsense, and describe ‘holes in fossil records’ as one of the major flaws in scientifically proven EVOLUTION THEORY

 

[reggieM]

… scientifically proven EVOLUTION THEORY

That should go up in a big sign with neon lights.

 

[itinerant1]

Are you actually serious? You believe in utter, unproved and poorly recorded nonsense, and describe ‘holes in fossil records’ as one of the major flaws in scientifically proven EVOLUTION THEORY

I like your sense of humor.

Evolution theory is awesome, despite its incompleteness. Evolution theory explains much about nature. It has expanded our understanding of nature tremendously.

However, I draw the line when it comes to the “mind” of man. Man’s intellect and will, that which radically separates him from higher animals and the anthropoid apes, cannot be accounted for by the natural processes of nature that accounts for the diversity and abundance of flora and fauna on this planet. Man’s body however, clearly has a history in these natural processes.

That will give you some idea as to where I agree and disagree on various views about biological evolution.

 

[hecd2]

Ayala contributing to the consensus sounds better to me. Ever since reading a transcript of his participation in a panel discussion, Ayala fascinates me. So I would like to follow his progress. Is that o.k.?

It’s not for me to say yes or no to that. Of course you should follow his progress if you wish.

Ayala’s work is very interesting and I highly recommend his recent book, in collaboration with Camilo Cela-Conde on Human Evolution.

Alec
evolutionpages.com

 

[Detales]

Thanks, jd, but that statement about Jesus was not a disparagement. It is simply how things are. We don’t really know if He was an actual person other than on pious grounds. And neither is offering alternatives, especially experiential Truth, a disparagement, except to those who might be fearful. In any case, l care neither way. My statements are informational.

Also, if you cannot differentiate clearly between ideologies, it is no wonder that everything I say seems to be “jargon” to you. All you really mean by that then is either “I don’t understand,” or “I don’t want to understand.” In fact, “I am confused by your lack of confusion.” is so far likely the most honest and accurate thing you have said.

Why is it that some people believe that they have experienced, or encountered something beyond the pale of mundane experience, that sets them apart from all others I don’t feel it sets me apart from others. It sets my informed experience apart from my ignorance. I am only offering that there may be such a “part” in everyone if they wish to take the care to explore it.

Why is it that only you (and - perhaps - a few others) are that special person to whom some grand vision has been given? Grand visions, jd, are given to those who care to look. Few do, therefore your impression.

Why is it that such “visions” are wrapped in a vernacular of mystery, that the lower men of this world are excluded from participation in by virtue of their abilities, or, rather, their inabilities? In fact, it is the vernacular of Clarity. As for abilities, I don’t know, jd; I didn’t make me. I just used what I was given as a gift to look beyond what I was served first. Are you allowing someone else to put their food preferences on your plate, or did you go see what else is on the hot table and dessert trays before you chose? Or did you chose at all?

I know you’re special, but, you’re not that special. “There is no greater or lesser in the Kingdom of God.” But that refers to the “I” that is “we.” It doesn’t refer to each ones particular gifts. No one can replace you, jd. You are unique before God. Each one is.

 

[Detales]

Hi Mom,

*Of course you like it. The idea that reality exists merely as an opportunity to exploit the senses, makes any responsibility beyond that notion void.

Do you wish to respond to my perhaps unwarranted provocation? *

I was with my Mentor for about thirty years. Do you suppose that that statement, one which I used to harmonize with someone else’s statement, is a fair and complete explication of his Standpoint and expressions in total? Are you that silly? Or do you just need to talk?

 

[MindOverMatter]

Are you that silly? Or do you just need to talk?

Why did you respond to my statement? You must really like me!

 

[Detales]

Perhaps, or not. But why do you think that “evolution” matters or not?

 

[grannymh]

… so which particular questions of his do you find interesting?
Alec
evolutionpages.com

This reply refers to Shi Huang’s paper “Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clad containing tarsiers.”

What was most interesting to me was that Huang was questioning the traditional molecular clock. There is no way I can determine if his conclusions are correct. It was the principle which I admired–reexamining a standing concept.

Huang innocently starting me thinking about the human bottleneck problem. What should be reexamined? In a way, the human bottleneck theory is similar to the molecular clock in that both, if viewed from a different perspective, could possibly deliver different results. Beginning with a definition of a bottleneck, the following progresses to a possible conclusion different from the consensus.

What exactly is a human bottleneck (reduced population)? The following is from a brief internet search.

From www.bbc.co.uk “With over 6 billion people living in the world today, human beings are a phenomenally successful animal. But our species, Homo sapiens, once came close to outright extinction.”

“Clues from genetics, archaeology and geology suggest our ancestors were nearly wiped out by one or more environmental catastrophes in the Late Pleistocene period. At one point, the numbers of modern humans living in the world may have dwindled to as few as 10,000 people.”

“Professor David Goldstein, a molecular biologist at University College in London, has uncovered evidence of a very ancient population bottleneck. A bottleneck is an event that reduces the genetic difference, or diversity, in a population of animals”

From Francisco J. Ayala, “The Myth of Eve: Molecular Biology and Human Origins”

“Neither the mtDNA results nor the ZFY results lead to the conclusion that narrow population bottlenecks consisting of one or very few couples have occurred in human ancestral history.”

In my humble opinion, the operating definition is – A human bottleneck (reduced population) is an event that reduces the genetic difference or diversity within the human population and which takes place sometime within the human population’s ancestral history.

Quite simply, the human bottleneck theory describes an event which had a specific action on the current human population sometime in their ancestral history.

Therefore, the human bottleneck theory is non-informative about the point of origin of the human species.

Therefore, the possibility of two sole parents of the human species does exist.

Blessings,
granny

The universe and all humanity are a joy to behold.

 

[Detales]

So if I understand correctly, there may have been a bottleneck, or there were two parents whose gene pool is interpreted as a bottleneck. Is there, then, any dating pertinent to the event in question, or human remains pre dating the event?

 

[antunesaa]

You made the argument that we cannot have confidence in the conclusions about human ancestry because palaeodemography is, in your words “hardly a field where people can replicate phenomena. All they can do is interpret data not produced in controlled experiments. So your statement seems unwarranted”. I was pointing out your fallacy of equating our inability to replicate phenomena in controlled experiments with an inability to reach high-confidence conclusions about them. The fact that the phenomenon in question cannot be replicated in controlled conditions is not in and of itself a barrier to reaching confident conclusions about it. This effectively removes another brick from the wall of your argument.

You also made the argument that my statement was “too assertive to be truly scientific” but as you have seen there are many assertive statements that are made in truly scientific publications.

Furthermore, your “common sense” is leading you astray. Do you know how the distance to SN1987A was measured? Do you know on what basis the conclusion that humans did not have two sole parents was reached? Unless you know these things, I don’t see how you can reasonably assert that we can hold either one more confidently than the other.

Alec
evolutionpages.com

Hi. On maths I think you and me have the same opinion. The Wiles episode underscores two different aspects: that open questions are difficult to solve; once solved, open questions become the consensus. In physics, things are much more difficult because testing the predictions of theory becomes more and more difficult. Sometimes it’s even difficult to identify what are the predictions… As we move away from maths, moving from an open question to a closed one becomes more and more difficult. In sociology, athropology, etc. I doubt there’s ever going to be any closed questions at all. While economics is almost exclusively mathematical and statistical today, I also doubt that there’s ever going to be positive consensus. Only negative ones: that Marxism economics leads nowhere, that totally liberal economies do not function well. That’s about it. The rest is an in-between, including biology and your “paleo-demographics”.

As for my friend, I didn’t tell her why I asked her these questions so I won’t publicize her identity here. But that’s beside the point, isn’t it? You either trust me or not. I trust you. If I had the time I would pursue this topic more, and probably cursorily review the literature accessible to me. But I haven’t and, as I told you, I don’t think it deserves the amount of time we are dedicating to it. But that’s just my opinion.

 

[antunesaa]

Just a couple more remarks about our debate. Concerning your point about the equivalence between an experimental result of modern physics and a particular hypothesis about a single bottleneck put forward by paleo-demographists and other people studying early humans, I must again stress that they’re by no means equivalent. The reason is that these two fields of knowledge have a very different praxis. Modern physics does very precise predictions about natural phenomena; in most cases, even the strangest predictions have been confirmed. In contrast, paleo-demographics cannot make such accurate predictions (because it is not supposed to). Therefore, any evidence (or theory) that it can produce is to be seen with a much, much larger grain of salt. (The same, for that matter, happens with economics or even medicine.)

To give you an example I am somewhat familiar with, there’s guys in economics that use the so-called Dynamic Stochastic General Equilibrium models. These models are supposed to capture the behavior of economic agents well enough so that they can be used to inform economic policy. There’s undreds of people using them right know in academia, at the FED, at the ECB, at the BoJ. Decisions made using them affect billions of people across the whole world. This framework is considered state of the art. However, if you ask knowledgeable people (such as Nobel prize winners Rob Lucas or Ed Prescott) about their merits, they’ll tell you they’re not useful because of particular theoretical flaws that have been well described. So, again, the non-verifiability of certain theories makes definitive assertions risky, at best, and probably foolish. And certainly reduce the likelihood you attach to those claims being true.

I think you must mean the unification of QCD and the electroweak force.

No, I mean unification of General Relativity and modern Quantum Mechanics.

How am I supposed to argue against some anonymous person’s opinion that is presented as a bare statement without any supporting rationale.

You are not supposed to argue with her because she isn’t in the slightest interested in our topic. I think she is a vague believer but I never talked with her about religion or philosophy.

Where is the fallacy in the primary literature?

I don’t know if there’s any. A fallacy is a flawed reasoning with a given purpose, so a theory might be formally right (that is, not fallacious), empirically correct (that is, agreeing with known data), but still be wrong.

Where is the paper that shows that the evidence is compatible with a human bottleneck of two individuals?

I don’t think she has bothered to look at this literature. She just thinks that, given our knowledge of genetics, you just cannot make such a definitive statement.

 

[grannymh]

As I said, I can give you more than twenty references to papers from a wide range of authors published over the last twenty years that investigate this question and unanimously conclude that the minimum bottlenecks in the human lineage are way above two individuals. Isn’t that consensus? Where is the paper that shows that the evidence is compatible with a human bottleneck of two individuals?

Alec
evolutionpages.com

That may be so. However, this is the short definition of bottleneck from the Berkeley, Understanding Evolution website: “An event in which a population’s size is greatly reduced.” It goes on to talk about genetic drift, gene frequencies, lost genes and founder effect.

Since a bottleneck is an event in a population’s history, it is non-informative about the point of origin of the fully completed human. Whether or not there were ever two or two thousand individuals as a reduced population in the time line of ancestral history is not the point. The point being the beginning of the time line.

Blessings,
granny

The universe is a joy to behold.

 

[hecd2]

This reply refers to Shi Huang’s paper “Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clad containing tarsiers.”

What was most interesting to me was that Huang was questioning the traditional molecular clock. There is no way I can determine if his conclusions are correct. It was the principle which I admired–reexamining a standing concept.

Nothing wrong with re-examining an accepted concept - but it needs a more knowledgeable approach than Huang’s to do it properly.

Huang innocently starting me thinking about the human bottleneck problem. What should be reexamined? In a way, the human bottleneck theory is similar to the molecular clock in that both, if viewed from a different perspective, could possibly deliver different results. Beginning with a definition of a bottleneck, the following progresses to a possible conclusion different from the consensus.

Well, no it doesn’t if we understand correctly what a bottleneck means. See below…

What exactly is a human bottleneck (reduced population)? … [Some of your content snipped for brevity]

In my humble opinion, the operating definition is – A human bottleneck (reduced population) is an event that reduces the genetic difference or diversity within the human population and which takes place sometime within the human population’s ancestral history.

Quite simply, the human bottleneck theory describes an event which had a specific action on the current human population sometime in their ancestral history.

Well yes. A bottleneck can occur any time in the ancestry of humans and that includes the history of species which are not Homo sapiens but are ancestral to Homo sapiens. Indeed, Ayala’s work probes human ancestry way before the emergence of Homo sapiens all the way back to the divergence of the human and chimpanzee lineages. Any bottleneck, including a bottleneck in human ancestry caused by a founder effect at the emergence of the Homo sapiens species would be detected.

Therefore, the human bottleneck theory is non-informative about the point of origin of the human species.

This is, I am afraid, not correct. Homo sapiens emerged after the divergence of the chimp and human lineages - in fact Homo sapiens appears at the earliest 200K BP whereas the divergence occurred at least 5M BP. So any severe reduction in the human population whether it was before, at or after the emergence of Homo sapiens would be detected. If humans had originated by the divergence of two individuals who give rise to a new species, Homo sapiens, then that would be genomically detected as an extreme bottleneck of two individuals in the human lineage. But such an extreme bottleneck is precluded by the evidence.

Therefore, the possibility of two sole parents of the human species does exist.

Not according to the genomic evidence, I’m afraid.

Alec
evolutionpages.com

 

[hecd2]

Hi. On maths I think you and me have the same opinion. The Wiles episode underscores two different aspects: that open questions are difficult to solve; once solved, open questions become the consensus.

Open questions might or might not be difficult to solve, but that is not the same as saying that open questions are rarely solved or that consensus is never reached (which is the basis of your argument). Every month, several conjectures in mathematics become theorems.

In physics, things are much more difficult because testing the predictions of theory becomes more and more difficult. Sometimes it’s even difficult to identify what are the predictions… As we move away from maths, moving from an open question to a closed one becomes more and more difficult

This is not necessarily true. Every week there are many results in physics presented which lead to consensus on something or other. You would know this if you read the primary literature. The same is true of most other branches of science from geology to molecular biology. These areas of consensus might refer to fundamental and extremely important things or smaller more detailed things - but these areas of consensus do emerge regularly. I could give you long lists of items of consensus in any natural science you care to mention. Your contention that questions are never or rarely settled in physics and maths, and never settled in molecular biology is simply wrong.

While economics is almost exclusively mathematical and statistical today, I also doubt that there’s ever going to be positive consensus. Only negative ones: that Marxism economics leads nowhere, that totally liberal economies do not function well. That’s about it

I’m sure what you say about economics is true, but economics is not science, so your example carries no weight.

The rest is an in-between, including biology and your “paleo-demographics”.

Are you really suggesting that there are no settled questions in biology, because that is patently false.

As for my friend, I didn’t tell her why I asked her these questions so I won’t publicize her identity here. But that’s beside the point, isn’t it? You either trust me or not. I trust you

It’s not beside the point and you don’t trust me - at least not in that way. You don’t trust me when I tell you that 20 peer reviewed papers written by the specialists in this field show that there is a scientific consensus on this subject (even though I can cite those papers), so why on earth do you expect me to trust you when you produce an anonymous friend as your “evidence”. The weight of evidence is all on my side. I trust that you have a friend who said something like what you reported, but I do not trust that you have asked the question fairly or that she has understood it correctly, I do not trust that she has read the relevant primary literature, in fact I do not trust that she actually knows anything about the specific subject. In short, unless she can show some specific problem with the actual papers that resolve this question, her opinion that the question cannot be resolved is no more than her personal incredulity and carries no weight whatsoever.

It is also telling that in all this discussion never once have you asked me to explain what the evidence is that has led to a consensus that human ancestors have not passed through a bottleneck of two. You have been content to rely on a false assertion that no such confident conclusion based on good evidence could possibly exist, and seem to have not the slightest curiosity as to why I (and those working in the field) disagree with you.

Alec
evolutionpages.com

 

[hecd2]

Just a couple more remarks about our debate. Concerning your point about the equivalence between an experimental result of modern physics and a particular hypothesis about a single bottleneck put forward by paleo-demographists and other people studying early humans, I must again stress that they’re by no means equivalent. The reason is that these two fields of knowledge have a very different praxis. Modern physics does very precise predictions about natural phenomena; in most cases, even the strangest predictions have been confirmed. In contrast, paleo-demographics cannot make such accurate predictions (because it is not supposed to). Therefore, any evidence (or theory) that it can produce is to be seen with a much, much larger grain of salt. (The same, for that matter, happens with economics or even medicine.)

Now that’s an example of a fallacious argument (and one moreover that is most likely to be made by someone who has not the slightest acquaintance with the subject matter of science except through the clouded lens of popular literature and prejudice). As I have pointed out, you are in absolutely no position to claim that the distance to SN1987A must be known with more confidence than the conclusion that humans did not pass through an ancestral bottleneck of two individuals unless you are familiar with the evidence and the arguments on which these two conclusions are based. Your claim that the statements of one field (physics) must necessarily be held with more confidence than those of another (genomics) is simply false. A single counter-example will suffice. Which of these two statements can we hold with more confidence?:

• Dark matter consists of 1000GeV neutralinos
• Chromosomes 2a and 2b in the common ancestor of the great apes fused to form chromosome 2 in the human lineage after the divergence of chimp and human lineages.

To give you an example I am somewhat familiar with, there’s guys in economics that use the so-called Dynamic Stochastic General Equilibrium models…

But we’re talking about natural science not economics so your example is moot.

No, I mean unification of General Relativity and modern Quantum Mechanics.

The same comments I made earlier about the unification of the electroweak force and QCD stand, only more so. You have chosen probably the most difficult problem in physics (and other difficult problems such as the one I referred to need to be solved first). Some hypotheses such as quantum gravity or M theories exist but have yet to be tested (or even make testable predictions). In this area, we are data poor and waiting for the LHC to disprove or encourage supersymmetry models. But this example of the difficulty in resolving the most difficult and fundamental problem that we know in physics doesn’t mean that we can’t reach confident conclusions about other subjects - and indeed there is consensus that both GR and QM separately make accurate predictions and are good models of large aspects of physical behaviour.

You are not supposed to argue with her because she isn’t in the slightest interested in our topic.

Then I am not in the slightest interested in her personal opinion on it which is worthless.

Alec
evolutionpages.com

 

[grannymh]

Nothing wrong with re-examining an accepted concept - but it needs a more knowledgeable approach than Huang’s to do it properly.

And how would you or anyone examine Shi Huang’s concept of maximum genetic diversity(MGD)?

Well yes. A bottleneck can occur any time in the ancestry of humans and that includes the history of species which are not Homo sapiens but are ancestral to Homo sapiens.

What I am looking for is the research that narrows down the “any time” above to the point of origin of the fully complete human species.

Indeed, Ayala’s work probes human ancestry way before the emergence of Homo sapiens all the way back to the divergence of the human and chimpanzee lineages.
Any bottleneck, including a bottleneck in human ancestry caused by a founder effect at the emergence of the Homo sapiens species would be detected.

In determining ancestor populations all the way way back, on what did Ayala and others base their reproduction rates? Ayala hedged his estimates in his 1995 paper by calling them rough approximations. Do not misunderstand me. I am not saying that estimates and approximations based on assumptions are wrong. Rather, I am saying that it is appropriate to use approximations because that is all there is to work with. Of course, the updated assumptions and methods are validated. Right?

I did find it interesting how Huang validated his assumptions and methods. His first steps appeared as common sense. But I am not qualified to evaluate his whole process.

If humans had originated by the divergence of two individuals who give rise to a new species, Homo sapiens, then that would be genomically detected as an extreme bottleneck of two individuals in the human lineage. But such an extreme bottleneck is precluded by the evidence.

Alec
evolutionpages.com

What exactly is the evidence that precludes a founder effect of two people?

In other words, do the computer-simulated populations used for exploring the minimum bottleneck size based on valid genetic evidence also keep track of the individual movements of 10,000 Homo sapiens who may or may not be fully complete humans? How does the computer determine that everyone of the 10,000 is incapable of wandering off?

What published research has studied the specific population before it became a reduced population bottleneck and determined that every member of that population was incapable of wandering off? What published research has evidence that during the time period following the bottleneck everyone was unable to wander off?

Unless there is actual evidence showing that no one could wander off at anytime from all the various populations of hominids, then the possibility of two sole parents of the human species does exist.

Blessings,
granny

All human life is sacred.

 

[hecd2]

• Chromosomes 2a and 2b in the common ancestor of the great apes fused to form chromosome 2 in the human lineage after the divergence of chimp and human lineages.

Doh! Not that it affects my argument, but for the sake of correctness that should be 2p and 2q.

Alec
evolutionpages.com

 

[hecd2]

And how would you or anyone examine Shi Huang’s concept of maximum genetic diversity(MGD)?

Exactly the same way as one would examine any hypothesis - look to see if it gels with the evidence. In this case, there are more problems with the concept than I can be bothered to go into here - as I said I wasted more time than I should have done looking into Huang’s claims. The concept doesn’t even make sense because he uses two ideas that turn out to be meaningless - his concept of complexity is bizarrely wrong, and his definition of genetic diversity is inconsistent and muddled. Worst of all, his claim that there is a limit to diversity which is tighter in more complex organisms is not borne out by the evidence. The man is a crank - as evidenced by his claim to have proven the Holy Grail of mathematics (the Riemann hypothesis) - in a paper without a single line of mathematics. As for his ideas about the great ape phylogeny - the less said the better.

What I am looking for is the research that narrows down the “any time” above to the point of origin of the fully complete human species.

There is no reason why there should necessarily have been a bottleneck at the origin of Homo sapiens. Since the method can detect an extreme bottleneck whenever it occurred, and no such bottleneck is detected, it doesn’t make sense to ask when the non-existent extreme bottleneck occurred.

In determining ancestor populations all the way way back, on what did Ayala and others base their reproduction rates? Ayala hedged his estimates in his 1995 paper by calling them rough approximations.

Ayala’s particular method which compares the allelic lineages of loci in the Major Histocompatibility Complex between human and chimp, and which precludes a bottleneck of two, does not depend on reproduction rates.

I did find it interesting how Huang validated his assumptions and methods. His first steps appeared as common sense. But I am not qualified to evaluate his whole process.

Well, the point is that he didn’t validate a thing - he cherry picked about seven genes from 25000 that seemed to support his idea, ignored any possible purifying or positive selection operating on them and claimed to have shown a new theory of evolution. Completely bonkers.

What exactly is the evidence that precludes a founder effect of two people?

It’s in those twenty papers that I cited for you. One very important finding is that humans and chimps share more allelic lineages than can pass through a bottleneck of two people, so it follows that there has not been a bottleneck of two in the human lineage (or in the chimp lineage for that matter).

In other words, do the computer-simulated populations used for exploring the minimum bottleneck size based on valid genetic evidence also keep track of the individual movements of 10,000 Homo sapiens who may or may not be fully complete humans? How does the computer determine that everyone of the 10,000 is incapable of wandering off?

What published research has studied the specific population before it became a reduced population bottleneck and determined that every member of that population was incapable of wandering off? What published research has evidence that during the time period following the bottleneck everyone was unable to wander off? Unless there is actual evidence showing that no one could wander off at anytime from all the various populations of hominids, then the possibility of two sole parents of the human species does exist.

All this business about wandering off is irrelevant - the research looks at the diversity in the genome of extant humans and its conclusions are relevant to human ancestors - not to extinct sideshoots (which have all gone through a bottleneck of zero!). In the ancestry of modern humans a bottleneck of two is precluded and two sole parents are not possible.

Alec
evolutionpages.com