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Mitchondrial DNA

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Jimlarmore

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We're talking about this link that you posted, right? My question is, do you understand that the results they describe are to be expected from evolution? That is, that the bacterium's cytochrome C should show about the same divergence from all the species they compared it to? The authors of that web page obviously think evolution predicts something else, but I think they are wrong. What do you think evolution predicts about these divergences? Please be specific. If they should all be the same, why did you post the link? If they should be different, explain why they should be different.


First off let's examine the predicate of the report : All bolding mine.
Cytochrome divergence
While it is one thing to argue the toss about the veracityof evolution on morphological grounds, an analysis of variations between proteins common to all species at least offers a quantitative basis against which the claims of neo-Darwinism can be evaluated - the anchor of mathematical objectivity.
One early discovery was that differences at the morphological level of a species are matched by variations in the amino acid sequences of common proteins. Percentage differences in cytochrome and haemoglobin for example increase with morphological distance. These differences are also consistent - all major vertebrate classes can be classfied on the basis of their protein sequences.
If we were to examine protein sequences from species related on the basis of standard evolutionary (morphological) assumptions we would expect to observe corresponding protein variation lending support to the hypothesis of lineal descent.

Here is an extract from the Dayhoff Atlas of Protein Structure and Function showing the molecular distance between the cytochrome C2 of the bacteria rhodospirillum rubrum and various eucaryotic chytochromes:


Before we look at any specifics I would like to say the author of this report is spot on with his logical presentation of divergence of speciational variations in the proteins of cytochrome C . So let's look at some specifics on the report that I think are significant.
Here is another extract giving cyclostome C sequence percentage differences between carp and selected terrestial vertebrates:
% diffCarp - fish13
13
14
13
13Horse - mammal
Rabbit - mammal
Chicken - bird
Turtle - reptile
Bullfrog - amphibian
And the divergence between the haemoglobin of a snail and selected vertebrate species:
% diffGastropod mollusk







Lamprey - cyclostome
Carp - fish
Frog - amphibian
Chicken - bird
Kangaroo - marsupial


In this box top table we see a percentage of only 13 percent between a carp and a horse, rabbit or chicken all of which are homotherms with massive differences in morphologies. This is a case that evolution would not predict.


God Bless
Jim Larmore

p.s. on edit: I copied and pasted from the website and the software here did not copy it the same way the table was laid out, so the information is not laid out properly. Please go to the site to examine them for clarity. Sorry​

 
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Jimlarmore

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When considering the divergence of proteins between species it's a good thing to remember that the same protein does not function the same way in all species at all. For instance the complex enzyme/protein insulin in humans is present in the earth worm ( annilida ) but has a totally different function in that animal than humans.

I Like to think that God used similar proteins to do different things the same way He caused the allele of one species to make bone in one and in the same area of another species that similar allele would make blood or hair. All of that looks to me to be part of intelligent design not a godless random thing.

God Bless
Jim Larmore
 
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gluadys

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In this box top table we see a percentage of only 13 percent between a carp and a horse, rabbit or chicken all of which are homotherms with massive differences in morphologies. This is a case that evolution would not predict.

On the contrary. This is exactly what evolution does predict for this case. The horse, rabbit and chicken lineages have all been separated from the carp lineage for the same length of time and have all accumulated approximately the same % difference in cytochrome c protein. Just as the theory of evolution would predict.

This is where it is important to know the principles of phylogeny and the nested hierarchy.

If you do not understand why these percentages are supposed to be similar, given the history of the lineages, then you really do not know evolution as well as you think you do.
 
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gluadys

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However, the beef with Darwin and evolution is whether new genomes are created.

Only among those who invent their own version of evolution, I think. This is strawman talk.

No one argues with microevolution here.

But they should. For all creationists claim to be comfortable with microevolution, they don't take time to learn how it works. They "believe" in it, but they don't understand it.

If you truly understood microevolution, you would understand the seamlessness of micro- and macro- evolution.

First of all, none of your examples would indicate a change in the number of base pairs that are characteristic of a distinct species.

So what? What makes that, rather than closed gene pools, a criterion of distinct species?

That is probably as good a boundard as there is between Darwinian evolution and the type of "evolution" that creationists are comfortable with.

The type of evolution creationists claim to be comfortable with IS Darwinian evolution. Drawing a distinction requires the creation of a strawman version of evolution.

Yes there are changes in genes that affect mating. Call it a new species if you want.

If the effect on mating is to eliminate genetic exchange between the respective gene pools, what else would you call it?

Again, you are just aiming to redefine "species" in vague enough terms that you can claim no speciation.

But, there is no successful mutation in evidence that is adding base pairs to genetic information.

Never claimed there was. Only that the two groups no longer form a single gene pool since they no longer mate with one another. If that is not the criterion of a species, what is?

As to what genetic differences accompanied the speciation, that is really here nor there. The genetic differences may or may not be the cause of the speciation. The refusal to interbreed is the immediate cause of the speciation irrespective of how much genetic change has occurred. One thing that is certain: whenever different populations no longer interbreed, for whatever reason, genetic differences will accumulate.

Breeding is dependent all types of morphology issues as chemical cues, if not colors for some animals.

Behaviour too, sometimes, such as breeding in different seasons, or even--with short-lived insects, at different times of day.

E.O Wilson describes a set of species that use chemical attractors. What distinguished one species from another (and prevented interbreeding) was not even a difference in the chemicals used, but a difference in the proportions of the chemicals used.

All these things can be changed by the deletion of information by mutation,

...also by the addition or substitution or duplication of information by mutation.

but none of these things prove the possibility that amphibians can become lizards or mammals.

Actually it does, for the process by which lizards and mammals diverged from amphibians is precisely the same process that gave us two separate populations of fruit flies.

Your example does not give any indication of bacteria beoming a multicellular organism

Because bacteria have never become multicellular. Only eukarya have developed multicellular forms. And they may have done so more than once. I expect the process of becoming multicellular does not follow the same procedure as cladisitic speciation though.


or fish becoming an amphibian.

Not my example, no, that just covers fruit flies in one experiment. But there are plenty of indications that amphibians diverged from fish.

Variations within a species that create distinct mating habits in certain populations is not proof that a new kind has been created.

Well, to determine that, you first need criteria to determine what a kind is. All science can point to is the emergence of new species. But that is all science needs.
 
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sfs

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Sort of like the guy on youtube you tries to support Dawkins with the Downs Syndrome example?
Since I haven't watched the YouTube video, it's hard to say for sure.

Why do you guys do this so consistently?
Do what? Try to figure out what you're talking about? I honestly don't know.

Again and again and again. You know what the question is and yet you try jerk us creationists around.
I don't know what the question is. I won't know what the question is until you explain it coherently. Are you unable to say what you mean by a "distinctly new" number? Just tell me what you mean.

Sarfati explains that your polyploidy is not beneficial mutation. It is not evolution. It is not a new genome.
Oh great. We're going to rely on Sarfati's knowledge of biology -- now there's a hole with no bottom.

And you alreay know what I am talking about.
No, I don't know what you're talking about, and I don't think you know either. You have some vague idea about the genetic differences between "kinds", but you have no real idea of what that means in terms of DNA. If it means something specific, you certainly haven't managed to say what it is.

[Sarfati (I assume) quote deleted.]

Well, Sarfati certainly managed to pack a lot of error, hand-waving and irrelevance into one passage, but that's not a skill I find particularly valuable. Should I take it that you now think the important difference between kinds is information, rather than the number of base pairs? If so, what definition of information are you going to use?

If I may recap. . . The genome of a species can grow and shrink over time; we know this because we can observe it happening. Genes within it can duplicate; we know this because we can observe it. The duplicates can accumulate mutations (where Sarfati gets the idea that one copy won't be expressed while mutations are occurring I have no idea); we can observe this. Two entire genomes can be combined, after which the combined pair will immediately start shedding large chunks of DNA, and also accumulating further mutations; we can observe this too. After any combination of these changes, the species may look dramatically different from the original species, be unable to breed with the original species, have a different number of genes, have differences in how genes are expressed and in the proteins that the genes make. And after all of these changes, we can tell that no real change has taken place because, well, because what? What is this mysterious thing that remains unchanged, and that defines the two species as part of the same kind? It can't be information, because the new species has a very different sequence of DNA than that found in any other organism, so it must have a different set of information.

So I'll ask you again: what are you talking about?

Is there one example of polypoidy in a trillion that might possibly beneficial and reproducible? I know Darwin likes and thrives on the long odds. But, lets see just one of those horses payoff.

Um, you are aware that polyploid speciation is extremely common in plants, right, and also sometimes occurs in animals? How can something be both immensely unlikely and yet be observed to occur routinely?
 
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sfs

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When considering the divergence of proteins between species it's a good thing to remember that the same protein does not function the same way in all species at all. For instance the complex enzyme/protein insulin in humans is present in the earth worm ( annilida ) but has a totally different function in that animal than humans.
That depends on the protein. Cytochrome C, in particular, has essentially the same function across all of life. (You can, for example, replace yeast cytochrome C with the rat version of the gene and it will still function.) This is one reason why cytochrome C is used in studies of evolution.
 
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sfs

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First off let's examine the predicate of the report : All bolding mine.

Before we look at any specifics I would like to say the author of this report is spot on with his logical presentation of divergence of speciational variations in the proteins of cytochrome C . So let's look at some specifics on the report that I think are significant.

No, the author is quite confused about evolutionary theory. Evolution does not predict that genetic (or protein) differences should simply be proportional to morphological differences. Evolution predicts that genetic difference should be proportional (possibly with some corrections for things like time between generations) to the branch length connecting the species. That is, imagine a tree where each twig tip is a current living species. Twigs that come from the same branch share a common ancestor. The total length of the branches connecting the twig tips represents the total time that mutational differences between the species have been accumulating, so the amount of genetic difference between the two species should be proportional to the branch length. If the branch distribution has some connection to morphological differences, that's great -- sometimes it does and sometimes it doesn't -- but it is the evolutionary relationship that matters.

In this case, the bacterium is at the end of one very long branch that goes all the way back to the trunk of the tree. All of the other species are various twigs on a different major branch of the tree. The total length between the bacterium and any of those species is going to be just about the same, and therefore the cytochrome C sequences should all be equally diverged. That is what evolutionary theory predicts, and is the basis for an enormous amount of work on molecular clocks.

You might also note that the web site you quote uses Michael Denton's book, which Denton himself now recognizes was wrong.​
 
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Jimlarmore

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On the contrary. This is exactly what evolution does predict for this case. The horse, rabbit and chicken lineages have all been separated from the carp lineage for the same length of time and have all accumulated approximately the same % difference in cytochrome c protein. Just as the theory of evolution would predict.

This is where it is important to know the principles of phylogeny and the nested hierarchy.

If you do not understand why these percentages are supposed to be similar, given the history of the lineages, then you really do not know evolution as well as you think you do.

I know making a prediction of only 13 % percent difference between animals with that great amount of morphological differences and physiology is lame to say the least using logic alone. You say this means I don't know evolution the way I think I do and you may be right. However, not accepting a false paradigm and it's attendent false studies does not mean I am not informed of what happened.

BTW, please show how a horse, rabbit or chicken could change only 13% from a carp over how many millions or billions of years and yet animals like bullfrog and a carp are 65% divergent. Use verifiable data or documentation to do it please.

God Bless
Jim Larmore
 
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Jimlarmore

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No, the author is quite confused about evolutionary theory. Evolution does not predict that genetic (or protein) differences should simply be proportional to morphological differences. Evolution predicts that genetic difference should be proportional (possibly with some corrections for things like time between generations) to the branch length connecting the species. That is, imagine a tree where each twig tip is a current living species. Twigs that come from the same branch share a common ancestor. The total length of the branches connecting the twig tips represents the total time that mutational differences between the species have been accumulating, so the amount of genetic difference between the two species should be proportional to the branch length. If the branch distribution has some connection to morphological differences, that's great -- sometimes it does and sometimes it doesn't -- but it is the evolutionary relationship that matters.

I've studied nested lineages and to be honest some of them just don't fit. The reason some of these things get placed the way they are is because they can't put them anywhere else. No, if you are going to use biochemical divergence then you need to show a time relation change in relationship to a change in morphology. Horses, rabbits and chickens are homotherms, fish are poikotherms. Horses, rabbits and chickens appeared a preposed several millions of years after fish did.Yet there is only a 13% divergence. Somehow though a bullfrog and a fish are not that far removed on the time scale but have a 65% divergence.

In this case, the bacterium is at the end of one very long branch that goes all the way back to the trunk of the tree. All of the other species are various twigs on a different major branch of the tree. The total length between the bacterium and any of those species is going to be just about the same, and therefore the cytochrome C sequences should all be equally diverged. That is what evolutionary theory predicts, and is the basis for an enormous amount of work on molecular clocks.

It's also the basis for a delusional way of determining the origin of the diversity in the biota.

You might also note that the web site you quote uses Michael Denton's book, which Denton himself now recognizes was wrong.

I didn't realize that. What part of Denton's work did he say was wrong friend. There's been several scientists who have waffled one way or the other after publishing their work , Behe is one of them. That does not mean their work was all wrong. Belief systems come and go the truth remains the same no matter what.

God Bless
Jim Larmore
 
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Mallon

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I'll just jump in here quickly and say that it's quite well known that amphibian genomes are somewhat more plastic than those of amniotes. This is why you can get cases of extreme polyploidy in some salamander species. Amphibian development and evolution just aren't as canalized as those of amniotes, and I suspect this would explain the greater genetic disparity between the frog and fish.
 
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Jimlarmore

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I'll just jump in here quickly and say that it's quite well known that amphibian genomes are somewhat more plastic than those of amniotes. This is why you can get cases of extreme polyploidy in some salamander species. Amphibian development and evolution just aren't as canalized as those of amniotes, and I suspect this would explain the greater genetic disparity between the frog and fish.
OK, what about the tuna and the lamprey? Both are fish aren't they? BTW, the platicity of the amphibians would need to be shown to prohibit or sustain the cytochrome c in divergence in these species.

God Bless
Jim Larmore
 
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sfs

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I know making a prediction of only 13 % percent difference between animals with that great amount of morphological differences and physiology is lame to say the least using logic alone. You say this means I don't know evolution the way I think I do and you may be right. However, not accepting a false paradigm and it's attendent false studies does not mean I am not informed of what happened.
You don't seem to be making an argument here. (Saying a claim is lame is not an argument.)

BTW, please show how a horse, rabbit or chicken could change only 13% from a carp over how many millions or billions of years and yet animals like bullfrog and a carp are 65% divergent. Use verifiable data or documentation to do it please.
You have misread the table. Yes, horse is 13% diverged from carp. Bullfrog and carp are not 65% divergent, however. Rather, both bullfrog and carp are 65% diverged from a particular bacterium.

Note that the horse/carp divergence represents a divergence time of ~430 million years, the time since the Silurian, when the ray-finned fish (ancestors of carp) diverged from the lobe-finned fish (ancestors of mammals). Bullfrog/bacterium divergence represent a much longer time, at least as long as the time since the prokaryote/eukaryote divergence. Exactly how long is hard to say, since the earliest eukaryotes are hard to pin down -- it could be anywhere from 1 to 3 billion years. So finding much greater divergence with bacteria is to be expected.
 
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sfs

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I've studied nested lineages and to be honest some of them just don't fit. The reason some of these things get placed the way they are is because they can't put them anywhere else. No, if you are going to use biochemical divergence then you need to show a time relation change in relationship to a change in morphology.
You may be getting tired of hearing this, but if you are going to argue against evolution, you really need to learn something about it. Currently you obviously don't, since what you say evolutionary theory predicts is simply wrong.

Look, this is a little silly. I'm a biologist, and I specialize in the genetics of evolution. I'm not asking you to believe in evolution just because I tell you to, but I am asking you to believe me when I tell you what the content of evolutionary theory is.

I didn't realize that. What part of Denton's work did he say was wrong friend. There's been several scientists who have waffled one way or the other after publishing their work , Behe is one of them. That does not mean their work was all wrong. Belief systems come and go the truth remains the same no matter what.
As far as I know he's never said his previous argument was wrong. Rather, he simply dropped the original argument and now argues that the interesting thing about cytochrome C divergences is that they reveal a constant rate of evolution over time. Completely different argument, and one that makes his previous argument nonsense.
 
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Assyrian

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Exactly how long is hard to say, since the earliest eukaryotes are hard to pin down -- it could be anywhere from 1 to 3 billion years. So finding much greater divergence with bacteria is to be expected.
Not to mention how rapidly bacteria reproduce which gives a lot more generations between them and the carp.
 
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gluadys

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I know making a prediction of only 13 % percent difference between animals with that great amount of morphological differences and physiology is lame to say the least using logic alone.

Not when you understand that the logic is not related to the morphology but to the point of origin of the differentiation between the lineages.

All of these are being compared to the carp. And all of them fall into the same nest as compared to the carp. The carp is a teleost fish, the others are all terrestrial vertebrates descended from a group of sarcopterygian fish. The relevant speciation is the one that gave rise to teleost vs sarcopterygian fish. And that occurred long before there were any horses, chickens, frogs or carp. Each of these are species found on either the teleost or the sarcopterygian branch, and as it happens, all but the carp are on the sarcopterygian branch.

So the carp is on one branch and all the others are on a different branch--the same different branch. The speciation which separates the frog from the carp is the same speciation which separated the rabbit from the carp and the horse from the carp and the chicken from the carp.

You say this means I don't know evolution the way I think I do and you may be right.

You don't. I'll illustrate from part of your answer to sfs. You said:

Horses, rabbits and chickens appeared a preposed several millions of years after fish did.Yet there is only a 13% divergence. Somehow though a bullfrog and a fish are not that far removed on the time scale but have a 65% divergence.

You are assuming that because the carp is a fish, it appeared when fish did. But that is not the case. The fish from which the lineage of terrestrial vertebrates diverged was an ancestor of the carp, not the carp itself. So the fish lineage has also been evolving and part of that 13% difference is due to the changes in the teleost line. So what you have to picture is a large V-shape like a tree that divides into two main trunks close to the ground. The carp, frog, chicken, rabbit and horse are all twigs high up in the branches. As it happens, the carp twig traces back to one trunk, all the others to the other trunk.

The degree of divergence of the carp from any and all twigs that go back to the other trunk is more or less the same. No matter whether you are tracing to the frog or the horse, you have to trace through all the smaller branches to the larger ones to the trunk on one side of the V, all the way down to where it meets the other, then all the way up it to the branches that lead to the smaller branches and twigs on that side.

However, not accepting a false paradigm and it's attendent false studies does not mean I am not informed of what happened.

You have lots of information, but it isn't organized to make sense.

BTW, please show how a horse, rabbit or chicken could change only 13% from a carp over how many millions or billions of years and yet animals like bullfrog and a carp are 65% divergent. Use verifiable data or documentation to do it please.

Go back to your own link and read the chart properly. The bullfrog was listed along with the chicken, horse and rabbit as having a 13% difference from the carp. The 65% difference was in comparison to the bacterium rhodospirillum. The horse, rabbit and chicken also showed 64-65% difference with the bacterium.

Ah, I see that error was already picked up by sfs.
 
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sfs

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Not to mention how rapidly bacteria reproduce which gives a lot more generations between them and the carp.
True, although the effect is smaller than you might think, since each generation of carp involves many rounds of cell replication, while bacteria only have one cell replication per generation. Since much mutation occurs during replication, this partly counteracts the different reproduction rates.

There are other effects, too. Bacteria have a larger population size than carp, which means that natural selection works more efficiently in bacteria. This means, at least when it comes to DNA in genes, that bacteria are more efficient at weeding out mildly deleterious alleles, which means their genes evolve more slowly per generation. (Look up the "nearly neutral theory of evolution" for details.)
 
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Jimlarmore

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You don't seem to be making an argument here. (Saying a claim is lame is not an argument.)

That's one way to conveniently deal with the observed disparity.

You have misread the table. Yes, horse is 13% diverged from carp. Bullfrog and carp are not 65% divergent, however. Rather, both bullfrog and carp are 65% diverged from a particular bacterium.

You are correct I stand corrected. However, there are still major areas of divergence that are hard to fit the evolutionary model here. I agree with the author of the report.

God bless
Jim Larmore
 
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Jimlarmore

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You may be getting tired of hearing this, but if you are going to argue against evolution, you really need to learn something about it. Currently you obviously don't, since what you say evolutionary theory predicts is simply wrong.

Look, this is a little silly. I'm a biologist, and I specialize in the genetics of evolution. I'm not asking you to believe in evolution just because I tell you to, but I am asking you to believe me when I tell you what the content of evolutionary theory is.

I have a degree in biology as well and mechanical engineering. I've studied ( several years ago ) the same things you have. I lost confidence in them when I started to specialize at that time in cytology. Even though what I learned is several years old the basic premise is the same. What you are tying to imply is that since I don't agree I just don't know what it's all about and that is just not accurate. I am not going to try to merge faith in the Bible and a false paradigm. You can't be a Bible Christian and totally buy into the mainstream paradigm of what macro-evolution teaches.

As far as I know he's never said his previous argument was wrong. Rather, he simply dropped the original argument and now argues that the interesting thing about cytochrome C divergences is that they reveal a constant rate of evolution over time. Completely different argument, and one that makes his previous argument nonsense.

I need to do a little more personal research into the cytochrome controversy to really make an educated response on this. It was a real buz word a few years back. I've read enough about it to reject it being a scaffolding system for evolving from a TTSS to a flagellum.

God Bless
Jim Larmore
 
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gluadys

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I have a degree in biology as well and mechanical engineering. I've studied ( several years ago ) the same things you have. I lost confidence in them when I started to specialize at that time in cytology.e


That maybe a reason to have questions about abiogenesis, but why couple that with suspicion of evolution?
 
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