Is the Human Brain the Null Hypothesis for Darwin's Theory?

[mark kennedy]

Only 29% of the genes in the comparison of the Chimpanzee Genome and the Human Genome sequences are the same. More importantly, with brain related genes I have yet to see one that had a beneficial effect. These are the effects most often seen:

Charcot–Marie–Tooth (CMT) sensorimotor neuropathy
Infantile spasms, dystonia, and other X-linked phenotypes
Schizophrenia
Brain tumors
Alzheimer's disease
Parkinson's disease​

Pick a chromosome, any chromosome and you will find a disease or disorder effecting the human brain as the result of a mutation.

Human Genome Project Landmark Poster

FIGURE 2. Comparative neuroanatomy of humans and chimpanzees. (Genetics and the making of Homo sapiens. Nature April 2003)

Charles Darwin in the preface to ‘On the Origin of Species’ credits Jean-Baptiste Lamarck with being the first man to propose that ‘the doctrine that species, including man, are descended from other species.’ This, Darwin argues, ‘being the result of law, and not of miraculous interposition.’ One of Darwin’s contemporaries, Gregor Johann Mendel, was doing a series of experiments with pea plants that yielded the laws of inheritance that would become the cornerstone of modern genetics. Darwin’s book popularized the idea of common decent while Mendel’s only surviving paper would not be rediscovered for nearly half a century later. Mendelian laws of inheritance became inextricably linked to waves of discovery starting with chromosome theory and culminating in the molecular basis of heredity: The DNA double helix. Darwinism contributed nothing to the waves of discovery but was philosophically commingled with genetics in what has become known as the modern synthesis.

In order to examine the scientific basis for common descent I propose to examine the genetic basis for the common descent of humans from that of apes. The most dramatic and crucial adaptation being the evolution of the human brain. Charles Darwin proposed a null hypothesis for his theory of common descent :

“If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” (Darwin, On the Origin of Species)​

With a cranial capacity nearly three times that of the chimpanzee the molecular basis for this giant leap in evolutionary history is still almost, completely unknown. Changes in brain related genes are characterized by debilitating disease and disorder and yet our decent from a common ancestor with the chimpanzee would have had to be marked by a massive overhaul of brain related genes. I propose that a critical examination of common descent in the light of modern insights into molecular mechanisms of inheritance is the single strongest argument against human/ape common ancestry.

Darwin discussed what he called the 'bane of horticulture', this was infertility. Haldane in 'The Cost of Natural Selection indicated "genetic deaths," which is either deaths or it's equivalents in reduced fertility. He said that it would take 300 generations for a beneficial mutation to become fixed with 1667 accrued in 10 million years.

Like Darwin, he used artificial selection to illustrate what would have had to happen in natural settings:

"especially in slowly breeding animals such as cattle, one cannot cull even half the females, even though only one in a hundred of them combines the various qualities desired." (Haldane, The Cost of Natural Selection)​

For us to have evolved from apes it would have required an accelerated evolution of brain related genes. The evolution of the human brain would have had to start it's accelerated evolution on a molecular basis some 2 million years ago and within Homo Erectus (considered human by most creationists) would have had a brain size twice that of the Austropihicene and early Hominids:

Early Ancestors:

A. Afarensis with a cranial capacity of ~430cc lived about 3.5 mya.
A. Africanus with a cranial capacity of ~480cc lived 3.3-2.5 mya.
P. aethiopicus with a cranial capacity of 410cc lived about 2.5 mya.
P. boisei with a cranial capacity of 490-530cc lived between 2.3-1.2 mya.
OH 5 'Zinj" with a cranial capacity of 530cc lived 1.8 mya.
KNM ER 406 with a cranial capacity of 510cc lived 1.7 million years ago.

(See Smithsonian Human Family Tree)

Homo Erectus Skulls:

Hexian 412,000 years old had a cranial capacity of 1,025cc.
ZKD III (Skull E I) 423,000 years old had a cranial capacity of 915cc.
ZKD II (Skull D I) 585,000 years old had a cranial capacity of 1,020cc
ZKD X (Skull L I) 423,000 years ago had a cranial capacity of 1,225cc
ZKD XI (Skull L II) 423,000 years ago had a cranial capacity of 1,015cc
ZKD XII (Skull L III) 423,000 years ago had a cranial capacity of 1,030cc

Sm 3 >100,000 years ago had a cranial 917cc

KNM-WT 15000 (Turkana Boy) 1.5 million years ago had a cranial capacity of 880cc

(Source: Endocranial Cast of Hexian Homo erectus from South China, AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006)

Homo habilis that would have lived. 2.5–1.5 mya with a cranial capacity of ~600 cc. The next link would have been Homo erectus with a cranial capacity of ~1000cc. KNM-WT 15000 (Turkana Boy) would have lived 1.5 mya and the skeleton structure shows no real difference between anatomically modern humans. The skull while smaller then the average cranial capacity of humans but close to twice that of his ancestors of 2 mya.

That means for our ancestors to have evolved it would have required a dramatic adaptive evolution of the size just under 2 mya sandwiched between two long periods of relative stasis. One such gene would have been the HARf regulatory gene involved in the early development of the human neocortex from 7 to 19 gestational weeks. With only two substitutions allowed since the common ancestor of the of 310 mya the divergence between humans and chimpanzees indicates 18 substitutions as early as 2 mya. (Nature, vol. 443, no. 7108, pp. 167-172 September 14, 2006)The ASPM gene while 99.3% the same for the human–chimpanzee comparison is marked by ten insertions/deletions equal to or longer than 50 bp, all of them located within introns. Primary microcephaly (MCPH) is a neurodevelopmental disorder characterized by global reduction in cerebral cortical volume.(Genetics, Vol. 165, 2063-2070, December 2003) In addition, a total of 2014 genes or ~10% of brain related genes analyzed differed in expression between humans and chimpanzees brains.(Genome Res. 14:1462-1473, 2004 ).

Evolutionists used to be able to use a 10 million year timeline, then it was 5 million years but when it comes to the most important adaptation you are looking at less then 1 million years and realistically it's only half that.

Darwin's null hypothesis for common descent is not unanswerable:

“If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” (Darwin, On the Origin of Species)​

If you take the road less traveled and choose to question common descent popularized by Darwin I submit that human brain evolution is prime topic. Darwin's theory is supposed to absolutely break down if a complex organ by decent with modification. My proposal is simply this, the human brain had neither the time nor the means to have evolved from that of apes.


Grace and peace,

Mark

 

[Mallon]

The genetic basis for the unprecedented expansion of the human brain from that of apes remains unknown to science and yet remains unquestioned.

What alternative explanation would you suggest, mark? And how could it be tested?

 

[MatthewDiscipleofGod]

What alternative explanation would you suggest, mark? And how could it be tested?

*Raises his hand* Oh, I know! I know! The Bible says... Wait, we can't rely on that! Forget that it has proven itself trustworthy with archaeology, fulfilled prophecy and accurate scientific type statements that were beyond normal comprehension at the time it was written.

 

[Mallon]

*Raises his hand* Oh, I know! I know! The Bible says... Wait, we can't rely on that! Forget that it has proven itself trustworthy with archaeology, fulfilled prophecy and accurate scientific type statements that were beyond normal comprehension at the time it was written.

No need to be sarcastic, brother. This is a fellowship forum, remember?
OK. So you suggest we use the Bible to explain "the unprecedented expansion of the human brain from that of apes". What explanation would that be, and more importantly, how could we test it (1 Th 5:21)?

 

[mark kennedy]

What alternative explanation would you suggest, mark? And how could it be tested?

Special creation is the only alternative to descent with modification and there is ample research in this area:

Creation and evolution, between them, exhaust the possible explanations for the origin of living things. Organisms either appeared on the earth fully developed or they did not. If they did not, they must have developed from preexisting species by some process of modification. If they did appear in a fully developed state, they must indeed have been created by some omnipotent intelligence, for no natural process could possibly form inanimate molecules into an elephant or redwood tree in one step (Science On Trial: The Case For Evolution, by Dr. Douglas J. Futuyma)​

Darwin offers a null hypothesis for his theory:

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case. No doubt many organs exist of which we do not know the transitional grades, more especially if we look to much-isolated species, round which, according to my theory, there has been much extinction. Or again, if we look to an organ common to all the members of a large class, for in this latter case the organ must have been first formed at an extremely remote period, since which all the many members of the class have been developed; and in order to discover the early transitional grades through which the organ has passed, we should have to look to very ancient ancestral forms, long since become extinct.(Darwin, On the Origin of Species)​

Darwin already indicated how this 'testable' null hypothesis would work.

1. An organ that could not have been formed by, 'numerous, successive, slight modifications.'
2. There has been little or no extinction.
3. Look to an organ common to all the members of a large class.
4. Discover the early transitional grades through which the organ has (or would have had to, emphasis mine) passed

My proposal is in the OP, your asking a question I already addressed

 

[Mallon]

Special creation is the only alternative to descent with modification and there is ample research in this area:

Creation and evolution, between them, exhaust the possible explanations for the origin of living things. Organisms either appeared on the earth fully developed or they did not. If they did not, they must have developed from preexisting species by some process of modification. If they did appear in a fully developed state, they must indeed have been created by some omnipotent intelligence, for no natural process could possibly form inanimate molecules into an elephant or redwood tree in one step (Science On Trial: The Case For Evolution, by Dr. Douglas J. Futuyma)
​

Darwin offers a null hypothesis for his theory:

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case. No doubt many organs exist of which we do not know the transitional grades, more especially if we look to much-isolated species, round which, according to my theory, there has been much extinction. Or again, if we look to an organ common to all the members of a large class, for in this latter case the organ must have been first formed at an extremely remote period, since which all the many members of the class have been developed; and in order to discover the early transitional grades through which the organ has passed, we should have to look to very ancient ancestral forms, long since become extinct.(Darwin, On the Origin of Species)
​

Darwin already indicated how this 'testable' null hypothesis would work.

1. An organ that could not have been formed by, 'numerous, successive, slight modifications.'
2. There has been little or no extinction.
3. Look to an organ common to all the members of a large class.
4. Discover the early transitional grades through which the organ has (or would have had to, emphasis mine) passed

My proposal is in the OP, your asking a question I already addressed

You seem to be saying that there is no way to test creation ex nihilo directly; that the only way to validate creation ex nihilo is to invalidate evolution, since you cannot possibly fathom a third alternative. You believe creation ex nihilo is right because evolution is wrong.
Is that correct?

 

[mark kennedy]

You seem to be saying that there is no way to test creation ex nihilo directly; that the only way to validate creation ex nihilo is to invalidate evolution, since you cannot possibly fathom a third alternative. You believe creation ex nihilo is right because evolution is wrong.
Is that correct?

Neither I nor Futuyma could since between the two they exhaust the explanations. The evidence for miracles that I have found most convincing do not interest skeptics in the slightest. Now since you choose to respond to the thread, I'm assuming in the interest of fellowship and open discussion, I would ask you to answer the question raised. Does the evolution of the human brain from that of apes qualify as a null hypothesis for Darwin's theory.

Answer or at least address the question artful dodger and I will be obliged to respond. I have told you what I think is testable and extensively tested in no uncertain terms. Now it falls on you to answer.

 

[mark kennedy]

*Raises his hand* Oh, I know! I know! The Bible says... Wait, we can't rely on that! Forget that it has proven itself trustworthy with archaeology, fulfilled prophecy and accurate scientific type statements that were beyond normal comprehension at the time it was written.

Your right you know, the fulfilled prophecy would be impossible by human agency. As history the Gospel of Luke and Acts would pass any litmus test for historic accuracy except for those pesky miracles academic types reject out of hand. Why can't we rely on the Bible for historical narratives? God has been neither silent nor absent in human history, who is it that can write him out?

Grace and peace,
Mark

 

[Mallon]

Now since you choose to respond to the thread, I'm assuming in the interest of fellowship and open discussion, I would ask you to answer the question raised. Does the evolution of the human brain from that of apes qualify as a null hypothesis for Darwin's theory.

Answer or at least address the question artful dodger and I will be obliged to respond. I have told you what I think is testable and extensively tested in no uncertain terms. Now it falls on you to answer.

Thanks for the reply, marc. Thanks also for calling me an "artful dodger". I'm not really sure why you called me that, but I can really feel the fellowship! At the risk of perpetuating the moniker, I guess I had better answer your question...
I'm not really sure what you're referring to when you say "Darwin's theory". If you're referring to Darwin's theory of evolution via natural selection, then no, I don't think that it's fair to say the evolution of the human brain from that of other apes qualifies as a null hypothesis of this theory. Evolution via natural selection posits that variation + heritability + differential reproduction = evolution. The evolution or non-evolution of the human brain in no way provides a test of this theory.
On the other hand, if you're referring to Darwin's theory that man descended from other apes, then yes, I think the null hypothesis works. The difficulty for ID proponents in testing this hypothesis, as I see it, is trying to distinguish between the current limits of our understanding of human brain evolution and genuine irreducible complexity. The two cannot be told apart. But I won't argue that here.

 

[mark kennedy]

Thanks for the reply, marc. Thanks also for calling me an "artful dodger". I'm not really sure why you called me that, but I can really feel the fellowship! At the risk of perpetuating the moniker, I guess I had better answer your question...

He's the guy who befriends Oliver Twist in the Dickens story, I used to call Arikay that but he didn't like it.Him and Azzirah Heep are my two favorite characters and I sometime toss it out there just for fun.

I'm not really sure what you're referring to when you say "Darwin's theory". If you're referring to Darwin's theory of evolution via natural selection, then no, I don't think that it's fair to say the evolution of the human brain from that of other apes qualifies as a null hypothesis of this theory. Evolution via natural selection posits that variation + heritability + differential reproduction = evolution. The evolution or non-evolution of the human brain in no way provides a test of this theory.

Darwin would seem to have suggested otherwise, in fact he said if an organ could not arise from a common ancestor his theory would completely break down. Now his example was the eye, personally I think the brain is a better focus since it's the key difference between man and ape.

Variation can come about through meiosis but only certain traits are variable. For a trait (I assume you mean an allele) to be inheritable it has to be in the germline or possibly in the very early development, at a time when mutations are the most dangerous. Differential reproduction seems reasonable but with hybrids infertility is a major problem and only a fraction of the population or cows, for instance, are suitable for that.

On the other hand, if you're referring to Darwin's theory that man descended from other apes, then yes, I think the null hypothesis works. The difficulty for ID proponents in testing this hypothesis, as I see it, is trying to distinguish between the current limits of our understanding of human brain evolution and genuine irreducible complexity. The two cannot be told apart. But I won't argue that here.

ID proponents simply don't address human origins in even the vaugest way. Apparently they are not seriously questioning it and it's my central concern. As far as testing it the data is rolling in on a regular basis, genomic comparisons would seem to be the latest development. It's actually being tested but they never question whether or not we share a common ancestor with apes.

There are two primary lines of evidence, Paleontology and Comparative Genomics. We are being told 2 mya our ancestors were little more then big chimpanzees who used rock tools. Within a couple a hundred thousand years they had migrated north to Lake Turkana where Homo erectus had a fully developed human frame and only a slightly smaller cranium.

There is neither the time nor the means for this and yet no one in the academic or scientific communite dares question it, not even ID proponents.

 

[Mallon]

There are two primary lines of evidence, Paleontology and Comparative Genomics. We are being told 2 mya our ancestors were little more then big chimpanzees who used rock tools. Within a couple a hundred thousand years they had migrated north to Lake Turkana where Homo erectus had a fully developed human frame and only a slightly smaller cranium.

There is neither the time nor the means for this and yet no one in the academic or scientific communite dares question it, not even ID proponents.

Perhaps the reason why none of the experts are willing to address the problem of the timing and mechanism of human brain evolution is because there is no problem. I'm not allowed to defend alternative views here, but can I ask if you've ever written the relevant experts about your concerns? If so, who did you write and how did they respond?

 

[mark kennedy]

You seem to be saying that there is no way to test creation ex nihilo directly; that the only way to validate creation ex nihilo is to invalidate evolution, since you cannot possibly fathom a third alternative. You believe creation ex nihilo is right because evolution is wrong.
Is that correct?

No it's not correct, I believe that the evolution of the human brain from that of apes is a null hypothesis for Darwinian evolution. You have again asked the same question that has already been answered and it's a rhetorical ploy, not an evidential approach to the subject of origins.

If you want positive evidence in support of an ex nihilo you have to look at the supportive evidence for the historicity of Scripture which is something I have never seen a skeptic do. I can get anti-creationist arguments all day long but when it comes to evidential logic evolutionists in general and TEs in particular resort to superficial rhetoric.

If you wish to pursue this formally, something I doubt very seriously, then you have only to ask. If you want to look at the positive evidence for an ex nihilo creation I warn you, it involves the reliability of the Scriptures as historical, primary source, documentation.

I'm not arguing in circles with you Mallon, either you want to take this seriously or I'm simply going to point out how highly conserved brain related genes are in reality. I know from extensive experience that you have nothing to counter except rhetoric and modernist philosophy.

Let's not go there.

 

[Mallon]

No it's not correct, I believe that the evolution of the human brain from that of apes is a null hypothesis for Darwinian evolution. You have again asked the same question that has already been answered and it's a rhetorical ploy, not an evidential approach to the subject of origins.

If you want positive evidence in support of an ex nihilo you have to look at the supportive evidence for the historicity of Scripture which is something I have never seen a skeptic do. I can get anti-creationist arguments all day long but when it comes to evidential logic evolutionists in general and TEs in particular resort to superficial rhetoric.

If you wish to pursue this formally, something I doubt very seriously, then you have only to ask. If you want to look at the positive evidence for an ex nihilo creation I warn you, it involves the reliability of the Scriptures as historical, primary source, documentation.

I'm not arguing in circles with you Mallon, either you want to take this seriously or I'm simply going to point out how highly conserved brain related genes are in reality. I know from extensive experience that you have nothing to counter except rhetoric and modernist philosophy.

Let's not go there.

I didn't come here to argue, mark. I came here to learn more about what you believe concerning human brain evolution, since I understand it as a particular hang-up of yours. I don't understand why you're acting so hostile, or why you feel the need to ignore some of my posts while responding to others twice. If you really don't want to have a respectful dialogue, just say so, and I'll leave.

 

[mark kennedy]

I didn't come here to argue, mark. I came here to learn more about what you believe concerning human brain evolution, since I understand it as a particular hang-up of yours. I don't understand why you're acting so hostile, or why you feel the need to ignore some of my posts while responding to others twice. If you really don't want to have a respectful dialogue, just say so, and I'll leave.

I don't understand why you ask the same question even when I answered it in the opening post. I've never seen anything like the TEs, they just never quit. They don't know the sciences and certainly have very little interest in theology but they never miss a chance to push their tired old rhetoric. This is how it works, you ask the question, whatever the answer you ask it again, and again, and again, pretending you don't understand.

I think you understand perfectly fine that the effects on the human brain genes are exclusively deleterious. I think you understand that there was neither the time nor the means for the human brain to have evolved from apes. I think you understand that Creationism is based on the historicity of Scripture and you refuse to discuss any of that for good reason, it blackballs you with secular humanists.

I think you are trying to throw a monkey wrench into the works which is all TEs seem capable of.

 

[mark kennedy]

Perhaps the reason why none of the experts are willing to address the problem of the timing and mechanism of human brain evolution is because there is no problem. I'm not allowed to defend alternative views here, but can I ask if you've ever written the relevant experts about your concerns? If so, who did you write and how did they respond?

You think they are unwilling but the fact is that they are unable to find the genetic basis for the evolution of the human brain from that of apes. If you want to transplant this thread somewhere else then be my guest, your secular friends don't have an answer either. I wouldn't bother trying to reach secular scientists with my objections to the a priori assumption of ape/human common ancestry, they are simply not allowed to question it. I did write the science editor of Time telling them that we are not 98% the same as chimpanzees in our DNA and, as expected, they ignored it.

The same lie has been over and over for so long no one is interested in correcting blatantly bad information.

 

[Mallon]

You keep accusing me of rhetorically asking you questions that you have already answered in the OP, but reading over this thread, I just don't see it, mark. I've asked questions in earnest, and in each of your replies you've called me an "artful dodger", you've accused me of not being serious, you've accused me of being dishonest and of subscribing to "modernist philosophy" (whatever that means). At this point, it's probably best that I drop out of this thread lest things become even more belligerent.

 

[mark kennedy]

You keep accusing me of rhetorically asking you questions that you have already answered in the OP, but reading over this thread, I just don't see it, mark.

It's in the title of the thread Mallon. You never answered the question and then no matter how many times I answer yours you just going to ask it again. The problem with TEs is they use cookie cutter tactics. That means I have seen it a hundred times and I am not running in circles because you are feigning a fellowship post.

I've asked questions in earnest, and in each of your replies you've called me an "artful dodger", you've accused me of not being serious, you've
accused me of being dishonest and of subscribing to "modernist philosophy" (whatever that means). At this point, it's probably best that I drop out of this thread lest things become even more belligerent.

I called you the artful dodger because you circumvented the question in the title, not even the opening post but the title asks a direct question. Then you will ask the same question again and again pretending you didn't get an answer. It's not the creationist that bears the burden of proof, it's the evolutionists since they have dominated academics and natural science for 150 years. They didn't stop there, Liberal Theology has supplanted traditional Christian theism and theology with a philosophy that is essentially deist.

You want to know why I don't think it's possible for an organ as complex and highly conserved as the human brain to evolve from that of apes? Ok, here are the known effects of mutations on brain related genes.

renal cystic diseases
Colorectal carcinoma
Alzheimer's
Lissencephaly and microcephaly

Pick a chromosome, any chromosome and you will find diseases and disorders that are the direct effects of mutations on the human brain.

Landmark Poster

Edited to add:

This is the null hypothesis, how would you test it?

Darwin already indicated how this 'testable' null hypothesis would work.

1. An organ that could not have been formed by, 'numerous, successive, slight modifications.'
2. There has been little or no extinction.
3. Look to an organ common to all the members of a large class.
4. Discover the early transitional grades through which the organ has (or would have had to, emphasis mine) passed

 

[shernren]

Here's a brief mathematical quibble: the proper meaning of the term "null hypothesis" as used in statistics has absolutely nothing to do with what mark is trying to argue. Having said that, I doubt anybody here actually cares what a real null hypothesis is, so I shall save my pedantry for some other time.

Just tagging so that I can keep up with what happens in this thread. ^^

 

[mark kennedy]

Here's a brief mathematical quibble: the proper meaning of the term "null hypothesis" as used in statistics has absolutely nothing to do with what mark is trying to argue. Having said that, I doubt anybody here actually cares what a real null hypothesis is, so I shall save my pedantry for some other time.

Just tagging so that I can keep up with what happens in this thread. ^^

Playing with the semantics again I see. One of the things that were not expected is the divergence being as high as it is. The obvious reason is the pleiotropy of mutations:

One critical parameter that affects the relative contribution of different genetic mechanisms to anatomical variation is the pleiotropy of mutations. In general, it is expected that mutations with greater pleiotropic effects will have more deleterious effects on organismal fitness and will be a less common source of variation in form than mutations with less widespread effects.Evolution at Two Levels: On Genes and Form​

 

[mark kennedy]

Why should he assume that all genetic variations represent "mutations?"

Absolutely not, in fact I get irritated with the word because I believe there are mechanisms that create new alleles (variations of the genes). I suspect it's some kind of an RNA strand or something but there is definitely something.

How do we know that any of these expressions were not found in Adam OR Eve or the sons of Noah or their wives? I am not sure how many genes you are talking about.

In the HAR (Human Accelerated Regions) they found 210 showing signs of major divergence. I really don't know how many brain related, protein coding and regulatory, genes would be involved but the simple answer is a lot.

In order to focus on human-specific changes that have functional importance, we first identified a set of genomic regions which are at least 100 bp in length and identical between chimp (P. troglodytes), mouse (Mus musculus), and rat (Rattus norvegicus) in at least 96% of alignment columns...Bioinformatic analysis of the 34,498 predicted functional elements shows that they are very similar to previously described highly conserved elements in the human genome. Only 19.6% overlap coding regions of human genes, while the remaining non-coding regions are mostly intergenic (45.4%) and intronic (31.0%)...
Forces Shaping the Fastest Evolving Regions in the Human Genome

By way of analogy, you can get a camry with four cyl. or six. In the factory of meiosis, things are created that are not "mutations", but are a different options packages.

Right, the genes cross over from the diploid chromosomes, one set from each parent. Obviously, that's not a mutation, traits being inherited in this way can even adapt to new environments but mutations are not required. I know certain genes can be turned off and on, I'm not really sure how that works exactly but I know it happens.

Crossing-over also occurs during meiosis I. Crossing over is an exchange of genetic material by non-sister chromatids of a homologous pair of chromosomes. This exchange of genetic material is the basis for additional variation in the offspring (another being the recombination of genetic material from two different genetic sources, the parents). This can lead to better adaptations and hence is a part of the process of evolution. Meiosis​

How do we know that the information that is optional did not reside in our ancestors and is not carried? That is a question, not a rhetorical question, since I don't know the answer.

A lot of times the scientists who research this sort of thing don't know. Here is an interesting example.

The finding grew out of a research project started three years ago in which Dr. Pruitt and Dr. Lolle were trying to understand the genes that control the plant's outer skin, or cuticle. As part of the project, they were studying plants with a mutated gene that made the plant's petals and other floral organs clump together. Because each of the plant's two copies of the gene were in mutated form, they had virtually no chance of having normal offspring.

But up to 10 percent of the plants' offspring kept reverting to normal. Various rare events can make this happen, but none involve altering the actual sequence of DNA units in the gene. Yet when the researchers analyzed the mutated gene, known as hothead, they found it had changed, with the mutated DNA units being changed back to normal form.
Startling Scientists, Plant Fixes Its Flawed Gene​

And Mark, what is the latest on where such information would be stored. One thing that research seems to show is that our simplistic notion of what the genetic code is seems to have a less defined boundary that was taught 20 years ago. Does the fact that you don't see the information in the strands of the 46 base pairs mean that the information isn't otherwise there? Remember that geneticists must rely upon notions like "self organizing", which implies that the information is present somewhere that we have no idea about.

The article above suggest the RNA may have had a copy somewhere:

Dr. Pruitt said he favored the idea that there is an RNA backup copy for the entire genome, not just the hothead gene, and that it might be set in motion when the plant was under stress, as is the case with those having mutated hothead genes.

He and other experts said it was possible that an entire RNA backup copy of the genome could exist without being detected, especially since there has been no reason until now to look for it.​

I kind of like this idea since they are finding out that the RNA is coming from all kinds of places that were previously thought to be junk DNA:

TANGLED GENES. In the classic view of the genome (top), individual genes were distinct segments of DNA that a cell transcribed into RNA whole and in one direction. New data show that multiple and overlapping genes can occupy a single strip of DNA that also produces several functional RNAs that don't encode proteins

The results from ENCODE were even more striking. In the slice of DNA studied in that project, between 74 percent and 93 percent of the genome produced RNA transcripts. What becomes of this tremendous output is uncertain. John M. Greally of the Albert Einstein College of Medicine in New York says it's likely that some portion of it is made accidentally and simply discarded. But the discovery that so much of the genome is being transcribed into RNA underscores how out-of-date the central dogma has become.
Mountains of new data are challenging old views