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Is evolutionary theory written in stone?

I have posted this elsewhere but thought it was worth saying . I have always loved science and have qualifications in the subject . However I do realise that science has its limitations . We should not worship science or think scientists and their work are infallible as all scientific theories are just our present thoughts on that particular matter. Unfortunately there are some people who appear to put science on a far higher realm of almost infallibility and do not appear to know that scientific theories which were once accepted as facts have gone to the wall in the light of further research.
In the case of Darwinism, there is an additional difficulty. Well, Charles Darwin wanted to offer an explanation of how the present forms of animal and plant life emerged, he found that some of the pieces of evidence in that argument were inevitably historical. Any attempt to verify the Darwinian theory of evolution requires knowledge of the past yet can the scientific method be actually applied to the study of the past? The point is that such a method must use presently accessible evidence to reconstruct what happened in the past . The problem lies with the degree of plausibility with which it can be done. So important was this difficulty that in 1976 Karl Popper expressed hesitation over whether the Darwinian theory of natural selection could strictly be said to fall within the scope of a scientific method and hence be deemed scientific in character.
Although many evolutionists now think this to be an overreaction based on a legitimate concern, there remains a significant degree of uncertainty and provisionality to any conclusions that are based on the past, precisely because we cannot directly access the earths past history .
It is interesting that even 'Darwin's Rottweiler', Richard Dawkins, sees this:
" Darwin may be triumphant at the end of the 20th century, but we must acknowledge the possibility that new facts may come to light which will force the successes of the 21st-century to abandon Darwinism or modify it beyond recognition ."
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newjaninev2 · 56-60, F
You might find that this has 'a degree of plausibility' (and I'll be interested in your multi-choice selection at the end)

Humans and chimpanzees both carry inactive genes acquired from viruses.
This occurs because some viruses insert a copy of their genome into the DNA of whichever species they infect. These are called retro-viruses... HIV is one such.

Where such viruses infect the cells that produce sperm and eggs, they can be passed on across generations.

The human genome contains thousands of these remnants of long-past infections... now rendered harmless... and so does the chimpanzee genome.

Most of them are in exactly the same place on both genomes.
That’s astonishing, so I’ll repeat it: most of them are on exactly the same place on both genomes.

Let’s choose an explanation from a few (non-exhaustive) options:

1. astonishing coincidence

2. when the gods created humans they decided to sprinkle around several thousand retro-viruses, and they put the preponderance of retroviruses at matching sites on both species because... umm... because... well... because... stop questioning the gods!

3. The majority of retroviruses match because both species inherited them from a common ancestor, who had itself accumulated them from the line of its own descent.

The small number which do not match are the remnants of infections that each species has warded off independently since divergence from the common ancestor... as predicted by the Theory of Evolution.
newjaninev2 · 56-60, F
Perhaps this too will have 'a degree of plausibility'

All species carry ‘silenced’ genes… these are genes that once caused certain proteins to be produced, but now no longer function in the original manner. Such genes are called pseudogenes.

Nearly all mammals have functional genes for expressing an enzyme (L-guluno-γ-lactone oxidase) that allows the production of vitamin C, which is essential for proper metabolism.

I say ‘nearly all mammals’ because primates cannot produce their own vitamin C. In humans, there is a set of four genes that code for vitamin C production. As you may know, these genes are composed of many, many smaller units called nucleotides, so these four genes contain a very large number of such nucleotides (the human genome has 64 billion nucleotides}. The first three genes are fully functional, but the final gene in the sequence has a mutation in a single nucleotide, and this mutation prevents the sequence from completing. That’s why humans need to obtain vitamin C from their food… because the mechanism for producing it has become a pseudogene.

Across all primates (chimpanzees, bononbo, humans, and apes) not only is it the final gene in the sequence that is silenced, but within that gene the same nucleotide carries the mutation that is responsible.

Now, why would this be?

1. astonishing coincidence

2. when the gods created all the species they put genetic pathways for vitamin C production into all mammals, but then inactivated a single nucleotide from among the four genes necessary for that production, inactivated the same nucleotide in all cases, and did that only in primates. They obviously thought this to be a tremendous joke to play, because we carry around 2,000 such pseudogenes.

3. All mammals developed the ability to produce vitamin C, but around 40 million years ago, in the ancestor common to all primates, that ability was removed by a mutation in a single nucleotide, and the deficit was passed to all primates due to common descent during evolution.
newjaninev2 · 56-60, F
Let's see if this has 'a degree of plausibility'

Embryology can be very helpful in showing how our evolutionary history appears during foetal development. There are a few quick and easy examples that spring to mind from all those available: gills, blood vessels, and kidneys.

In the early stages of development, fish embryos have a series of pouches (separated by grooves) near where the head will later develop. These are called the brachial arches - they develop into gills, and the grooves between them develop into the gill slits. It‘s very straightforward.

Other vertebrates have the same structures... including humans. In fact, I once had the opportunity to see these brachial arches for myself on a foetus, and it was fascinating. They‘re not ‘sort of like’ a fish‘s brachial arches... they are a fish‘s brachial arches. They‘re morphologically completely identical.

Tiktaalik roseae, on the cusp between ocean and land, used gills and lungs, but after the move onto land, gills were superfluous (although Olympic swimming competitions would be very different had we retained them). Sometimes (it‘s very rare) the gill slits fail to close, but it‘s easily corrected via minor surgery once the infant is born.

Blood vessel development in fish is, once again, basic and straightforward, producing six major blood vessels. In mammals (including humans, of course), the same six major blood vessels appear in early foetal development, but then three of them disappear at the same time that our circulatory system stops resembling that of fish and instead becomes identical to the circulatory system of embryonic amphibians. Not similar... identical.

In amphibians, this system simply grows into an adult amphibian circulatory system, but in mammals (including humans, of course) it changes into the circulatory system of embryonic reptiles. Not similar to the circulatory system of embryonic reptiles... identical.
In reptiles, this system simply grows into an adult reptilian circulatory system, but in mammals (including humans, of course), it undergoes further changes (the development of carotid, pulmonary, and dorsal arteries) to become the mammalian circulatory system.

During development, human embryos form three distinctly different types kidneys... the pronephros, the mesonephros, and the metanephros. The first two systems are discarded. The pronephros is the kidney system found in fish and amphibians, the mesonephros is the kidney system found in reptiles, and the metanephros is the kidney system that we eventually use.

From fish to amphibian to reptile to mammal.
No matter how many comforting myths we mutter to ourselves, every foetus carries the truth.
newjaninev2 · 56-60, F
Let's continue our search for 'a degree of plausibility'

Genes code for proteins. That’s pretty much all they do (they have quite dull social lives, and don’t seem to have hobbies or outside interests). Those proteins are built up from amino acids.

The genes comprise large numbers of base-pairs, which are simply guanine matched with cytosine and adenine matched with thymine. The human genome contains around 3.2 billion of these base pairs (the largest we’ve found so far is that of the flowering plant Paris japonica, which has 150 billion base pairs. The marbled lungfish has 133 billion base pairs).

As I said, proteins are built up from amino acids. Each amino acid that is used to build the proteins is specified by three base-pairs (those blocks of three base-pairs are called codons).

Let’s look at cytochrome c (we could use any number of such proteins, but I have a fondness for cytochrome c… I like the alliteration)

The cytochrome c protein is built up from around 100 amino acids.
This means that there are 10E135 possible ways that the amino acids could be arranged… but not all of those arrangements would work, of course.
However, because there’s a high level of redundancy in the construction of cytosine c (and all proteins), a stunning 10E93 variants would still be functional.
So that’s 100,000,000,000, 000,000,000, 000,000,000, 000,000,000, 000,000,000, 000,000,000, 000,000,000, 000,000,000, 000,000,000, 000,000,000 possible ways that DNA could code for functional cytosine c.

Time to make some predictions in accordance with the Theory of Evolution, don’t you think?

1. Because evolution began from a tightly limited range of organisms, only one of those possible functional variants will have been passed down over the last 3.5 billion years.

2. Because of point mutations (among other factors), there should be evidence of extremely slight variation that has crept in over the last 3.5 billion years… after all, even high-fidelity copying systems aren’t perfect (and it would be suspicious if they appeared to be so)

3. That variation should be negligible for species that have comparatively recent common ancestors, and increase between species with more distant common ancestors… while still remaining negligible (The process is remarkably stable, so we wouldn’t expect too many of the 10E93 functional variants to have appeared).

So, what do we find?

How many amino acid differences are there between humans and other species?
To make things interesting, let’s list some species in order of how long it has been since we shared a common ancestor with each species, and then see how many amino acid differences there are between us and that species.
Chimpanzee = 0
Rhesus Monkey = 1
Rabbit = 9
Cow = 10
Pigeon = 12
Bullfrog = 20
Fruit Fly = 24
Wheat Germ = 37
Yeast = 42

Evidence-based simplicity and elegance… the Theory of Evolution by Natural Selection
Speedyman · 70-79, M
It's touching your faith in these things and what you read. However I'm just in the process of reading a paper by geneticist who quites almost the same evidence as you do but comes to a different conclusion. I know it's your pet theory that we come from nothing, we are going to nothing, And there is no point in us being here while we are here as we are simply products of evolutionary chance. Unfortunately some scientists are not nearly as convinced that you appear to be that this theory is cut and dried. But if it gives you comfort then you believe it@newjaninev2
newjaninev2 · 56-60, F
@Speedyman Lose the burble... just respond to the comments I wrote, and please try to respond in a meaningful way.

Please be specific.

I have no time for unspecified papers written by unspecified geneticists and unspecified conclusions
Speedyman · 70-79, M
You are quite a fanatic aren't you? But as I say if it makes you happy then you believe it. You are going nowhere you've come from nowhere and there's no point in your life while you are here so I hope you find that very comforting . You are merely a chance collection of chemicals and your life has no value whatsoever@newjaninev2
newjaninev2 · 56-60, F
@Speedyman Oh, I'm sorry... did you say something?

Oh no, apparently not.
Just more of the same irrelevant mumbling.

For a second there I thought you might have finally responded to the comments I posted yesterday and this morning... but no
Speedyman · 70-79, M
I have responded to them and they prove nothing unless you take on board the assumptions you make. You can't seem to see that the point you're making depend on making certain assumptions. But then I wouldn't expect you to say anything apart from your own fundamentalist fanaticism@newjaninev2
This message was deleted by the author of the main post.
SW-User
@newjaninev2 Very educative. Always a pleasure to read your responses. Thanks