What is peer review?

[Sherlock Holmes]

Often when debating atheism or questioning the evolution doctrine, the supporters of evolution will reject arguments against it made by scientists because they insist that only "peer reviewed" publications are to be trusted (else it must be pseudo science).

So I want to ask how does one decide whether a journal is or is not peer reviewed? what definition do people use to help them make this decision?

[Jose Fly]

So tell me....how much time have you devoted to studying genetics (molecular and/or population)?

I never kept track, why do you ask? are you seeking to challenge me on some point? that's fine but perhaps a dedicated thread is best?

How about a rough estimate (e.g., have you studied genetic for years, months, days, hours) and some examples of what you've studied (e.g., classes you've taken, books you've read, genetics work you've done)?

[Sherlock Holmes]

So tell me....how much time have you devoted to studying genetics (molecular and/or population)?

I never kept track, why do you ask? are you seeking to challenge me on some point? that's fine but perhaps a dedicated thread is best?

How about a rough estimate (e.g., have you studied genetic for years, months, days, hours) and some examples of what you've studied (e.g., classes you've taken, books you've read, genetics work you've done)?

No, I can't meaningfully estimate the time. I read a lot, often in deep dives, bursts, perhaps three of or four books sometimes. Then I might move to some other subject or not read for months.

[The Barbarian]

The cube is an analogy for the much more complex DNA molecule

It's a very faulty model, as you just learned. I get that you would like us to believe genes can be modeled on a Rubik cube, but you now know that won't work.

so you are insisting that the human genome (a very complex molecular data store) can be reached from a worm genome

No. Remember when I (and others) told you that not understanding how evolution works, is constantly tripping you up? It just took you down again. You're thinking of descent as a ladder; it's a bush. Humans did not evolve from nematodes; both evolved from a common ancestor. Hence the 52 amino acid differences in cytochrome C between them represents about 26 total mutations in each line. You missed something else important; I left a hint, but you don't seem to have realized it.

under the influence of nothing but natural forces.

No sign of magic anywhere. Sorry.

But those laws of chemistry and mutability and so on, like a Rubik's cube's laws of legal possible manipulations, could also have such behavior that they too make certain outcomes impossible - you merrily assume this cannot happen.

Well, that's a testable assumption. Show me one gene that could not have been produced by mutation of a different gene.

My dear fellow, I have not asserted that the human genome cannot be reached from a prehistoric worm genome,

That was a separate error on your part. See above. But you've now retreated to admitting that there is no proof against common descent? We're making progress.

You assert that it can

And as you just learned, the structure of cytochrome C shows evolutionary connections between humans and nematodes. And as you now realize, the difference in the two forms of cytochrome C are those that are caused by processes which observably happen in nature. These different sorts of mutations are being constantly observed, so we have proof of the way these changes happen. But it's better than that...

We can get a phylogeny from the different forms of cytochrome C in different taxa, which gives us the same phylogeny as obtained by DNA, the fossil record, and other evidence...

Describing the difference between two configurations does not prove that one configuration is reachable from the other,

But showing that the differences are those that are the result of processes observed to happen, is compelling evidence for such evolution. As is this diagram, showing fewer differences between organisms with more recent common ancestors. Precisely what evolutionary theory predicts, but an impossible problem for creationism.

Your entire Rubik cube story is based on superficial, naïve extrapolation, just as would be the claim that the observed phylogeny of cytochrome C mutations were instead magically inserted rather than evolved.

And the part you missed? You see every element in your Rubik cube is essential and locked into a very limited number of possible changes, while genes have much wider ranges of possible change. But there's this, too; all cytochrome C molecules work the same way. How could there be so many changes without changing the function of the molecule? It turns out that most of the amino acids in a protein can be changed out in various ways without changing the function of the molecule. But a few regions where the activity is mediated, cannot change. So we have constant and variable regions of the molecule; the mutations happen in the variable regions.

This makes no sense, except in evolutionary terms. Which is something even James Tour should have realized, but for some reason, does not.

[The Barbarian]

It seems to me that the idea that getting a PhD is all there is to being a scientist, is faulty thinking. It's even less reasonable to suppose that if one has a PhD in something, that one is thereby an expert in something else.

We have seen here, the example of a PhD biochemist who doesn't even know what evolution is. He might be a great chemist, but he's a pathetically bad biologist.

This is a revelation, biology, genetics, DNA, cell replication, protein synthesis etc, etc, etc does not involve chemistry??

In the sense that being a lawyer involves being able to read and write. But that isn't sufficient to understand the law.

and you say he doesn't understand!

According to you, Tour says he doesn't understand. And then he proved that assertion; he thinks evolution is about the origin of life. It's not something he'd have to know as false to be a biochemist, but almost all biochemists do know that belief is false.

I really think its telling that you tout an "authority" on these areas when said "authority" admits he doesn't understand the subject, and then provides us with proof that he does not.

[Jose Fly]

How about a rough estimate (e.g., have you studied genetic for years, months, days, hours) and some examples of what you've studied (e.g., classes you've taken, books you've read, genetics work you've done)?

No, I can't meaningfully estimate the time. I read a lot, often in deep dives, bursts, perhaps three of or four books sometimes. Then I might move to some other subject or not read for months.

So you've read books on genetics? Which ones?

[Jose Fly]

And the part you missed? You see every element in your Rubik cube is essential and locked into a very limited number of possible changes, while genes have much wider ranges of possible change. But there's this, too; all cytochrome C molecules work the same way. How could there be so many changes without changing the function of the molecule? It turns out that most of the amino acids in a protein can be changed out in various ways without changing the function of the molecule. But a few regions where the activity is mediated, cannot change. So we have constant and variable regions of the molecule; the mutations happen in the variable regions.

This makes no sense, except in evolutionary terms. Which is something even James Tour should have realized, but for some reason, does not.

Ah, functional redundancy and cytochrome C.....something I've not seen a creationist offer any sort of meaningful rebuttal to.

[Sherlock Holmes]

The cube is an analogy for the much more complex DNA molecule

It's a very faulty model, as you just learned. I get that you would like us to believe genes can be modeled on a Rubik cube, but you now know that won't work.

What won't work? Rest assured group theory is applicable and has been applied to genetics and genome evolution, would you like to me show you?

The Rubik cube is the analogy, it's "evolution" over time forms a group (that's defined here for you) do you not agree?

so you are insisting that the human genome (a very complex molecular data store) can be reached from a worm genome

No. Remember when I (and others) told you that not understanding how evolution works, is constantly tripping you up? It just took you down again. You're thinking of descent as a ladder; it's a bush. Humans did not evolve from nematodes; both evolved from a common ancestor. Hence the 52 amino acid differences in cytochrome C between them represents about 26 total mutations in each line. You missed something else important; I left a hint, but you don't seem to have realized it.

under the influence of nothing but natural forces.

No sign of magic anywhere. Sorry.

No, I'm thinking of a worm, read and takes notes, these might come in handy later:

Humans evolved from a five-centimetre-long worm-like creature that wriggled in the sea more than 500 million years ago, scientists have learned.

The extinct Pikaia gracilens has been confirmed as the oldest known member of the chordate family, which includes all modern vertebrates including humans.

From: Humans evolved from worm creature

or

“The discovery of myomeres is the smoking gun that we have long been seeking,” said the study’s lead author, Professor Simon Conway Morris of the University of Cambridge. “Now with myomeres, a nerve chord, a notochord and a vascular system all identified, this study clearly places Pikaia as the planet’s most primitive chordate. So, next time we put the family photograph on the mantle-piece, there in the background will be Pikaia.”

From: Human's oldest ancestor found

(Let me know if I'm moving too fast for you).

But those laws of chemistry and mutability and so on, like a Rubik's cube's laws of legal possible manipulations, could also have such behavior that they too make certain outcomes impossible - you merrily assume this cannot happen.

Well, that's a testable assumption. Show me one gene that could not have been produced by mutation of a different gene.

My dear fellow, I have not asserted that the human genome cannot be reached from a prehistoric worm genome,

That was a separate error on your part. See above. But you've now retreated to admitting that there is no proof against common descent? We're making progress.

The error is entirely yours, you claim humans did evolve from worms (see above) and your argument for that is that we have no proof that they cannot.

As you are now learning he who states a proposition carries the burden of proof for supporting it and you have offered no proof that the Pikaia genome can ever develop into the human genome under the influence of just natural forces and time, it is supposition.

As a simple example from group theory (exemplified in this case by a Rubik's cube whose legal conformations from a group) shows, in some cases not all conceivable conformations can be reached from some other conformation using just the rules of permutation for the group.

You assert that it can

And as you just learned, the structure of cytochrome C shows evolutionary connections between humans and nematodes. And as you now realize, the difference in the two forms of cytochrome C are those that are caused by processes which observably happen in nature. These different sorts of mutations are being constantly observed, so we have proof of the way these changes happen. But it's better than that...

We can get a phylogeny from the different forms of cytochrome C in different taxa, which gives us the same phylogeny as obtained by DNA, the fossil record, and other evidence...

Describing the difference between two configurations does not prove that one configuration is reachable from the other,

But showing that the differences are those that are the result of processes observed to happen, is compelling evidence for such evolution. As is this diagram, showing fewer differences between organisms with more recent common ancestors. Precisely what evolutionary theory predicts, but an impossible problem for creationism.

The "evolutionary connections between humans and nematodes" are inferred "connections" made on the assumption one evolved from the other! In plain speak "If we assume humans evolved from nematodes then we can prove that humans evolved from nematodes".

There might be a host of reasons why structural similarities exist in nematode DNA and human DNA, these can only be regarded as evidence for evolution if you can prove there's no other way for these similarities to arise, but like much of evolution it is not proved it is assumed.

Your entire Rubik cube story is based on superficial, naïve extrapolation, just as would be the claim that the observed phylogeny of cytochrome C mutations were instead magically inserted rather than evolved.

Funny, quite revealing, how the very suggestion that such similarities might have a non evolutionary cause is simply incomprehensible to you. The facts are that if we assume evolution can do what is claimed then yes the similarities are evidence for evolution, but we cant then use that similarity to say "Hey look, this proves evolution". Trust me, I'm a detective as you know and logic is my forte, you've likely been hoodwinked here, many have.

And the part you missed? You see every element in your Rubik cube is essential and locked into a very limited number of possible changes, while genes have much wider ranges of possible change.

Yes this is true, but the discussion is actually about groups, the cube is just a visual aid to discussing a simple example of group theory showing how members of a set when combined (using a set of rules) to generate new members can sometimes lead to closure, that is no matter how many times we apply the group mapping (function) to members we can never generate certain outcomes. We can replace the cube with more complex examples with much larger states spaces, but the concept of a closed group is not limited to the size of the state space. It is complex, non-intuitive and based on sometimes complicated rules.

To assume that the genome we see in biological organisms is unrestricted is just an assumption. If closure is present then evolution might not be possible, not in the unbounded way it is assumed to. This is all I am saying and none of it is unreasonable, this is a valid scientific question.

But there's this, too; all cytochrome C molecules work the same way. How could there be so many changes without changing the function of the molecule? It turns out that most of the amino acids in a protein can be changed out in various ways without changing the function of the molecule. But a few regions where the activity is mediated, cannot change. So we have constant and variable regions of the molecule; the mutations happen in the variable regions.

This makes no sense, except in evolutionary terms. Which is something even James Tour should have realized, but for some reason, does not.

If the mutations are random why are they confined to regions at all?

[Difflugia]

No, I can't meaningfully estimate the time. I read a lot, often in deep dives, bursts, perhaps three of or four books sometimes. Then I might move to some other subject or not read for months.

So you've read books on genetics? Which ones?

[DrNoGods]

[Replying to Sherlock Holmes in post #137]

Yes this is true, but the discussion is actually about groups, the cube is just a visual aid to discussing a simple example of group theory showing how members of a set when combined (using a set of rules) to generate new members can sometimes lead to closure, that is no matter how many times we apply the group mapping (function) to members we can never generate certain outcomes. We can replace the cube with more complex examples with much larger states spaces, but the concept of a closed group is not limited to the size of the state space. It is complex, non-intuitive and based on sometimes complicated rules.

What do you mean "the concept of a closed group"? A mathematical group has closure as one of its fundamental properties ... no closure, no group. To form a group a set has to have the following properties (from the Wolfram link you used, or any abstract algebra book):

1. Closure: If A and B are two elements in G, then the product AB is also in G.

2. Associativity: The defined multiplication is associative, i.e., for all A,B,C in G, (AB)C=A(BC).

3. Identity: There is an identity element I (a.k.a. 1, E, or e) such that IA=AI=A for every element A in G.

4. Inverse: There must be an inverse (a.k.a. reciprocal) of each element. Therefore, for each element A of G, the set contains an element B=A^(-1) such that AA^(-1)=A^(-1)A=I.

If the commutative property holds (AB = BA) then it is called an Abelian group.

Closure is a requirement though, or it isn't group. Closure doesn't mean "no matter how many times we apply the group mapping (function) to members we can never generate certain outcomes." It means that a group operation on any set of elements has to produce another member of the group (ie. #1 above). It isn't complex, or non-intuitive, or based on complicated rules. An algebraically closed group has the same basic property (Group A is algebraically closed if every finite set of equations and inequations that has coefficients in A and is consistent with A has a solution in A).

If anyone wants the gory details on the Rubik cube group see this:

http://math.fon.rs/files/DanielsProject58.pdf

Are you trying to pull the wool over our eyes by claiming that group theory suggests something about evolution and how DNA works is wrong? It doesn't.

[The Barbarian]

The cube is an analogy for the much more complex DNA molecule

It's a very faulty model, as you just learned. I get that you would like us to believe genes can be modeled on a Rubik cube, but you now know that won't work.

What won't work?

Your attempt to model genetics on a Rubik cube. It's hilariously flawed.

Rest assured group theory is applicable and has been applied to genetics and genome evolution, would you like to me show you?

Kinetic theory applies to genes and Rubik cubes, too. But you still can't map genomes and mutations onto Rubik cubes.

so you are insisting that the human genome (a very complex molecular data store) can be reached from a worm genome

No. Remember when I (and others) told you that not understanding how evolution works, is constantly tripping you up? It just took you down again. You're thinking of descent as a ladder; it's a bush. Humans did not evolve from nematodes; both evolved from a common ancestor. Hence the 52 amino acid differences in cytochrome C between them represents about 26 total mutations in each line. You missed something else important; I left a hint, but you don't seem to have realized it.

under the influence of nothing but natural forces.

No sign of magic anywhere. Sorry.

No, I'm thinking of a worm,

No, you're not.

Humans evolved from a five-centimetre-long worm-like creature that wriggled in the sea more than 500 million years ago, scientists have learned.

It's not worm-like. It's a chordate. An animal in the same phylum as we are. It's no more a worm than you are.

Worms are polyphyletic, but they do not include deuterostomes. (we are among the phyla in the deuterostomes)

Worms: Phyla Platyhelmintes, Nematoda, and Annelida
https://manoa.hawaii.edu/exploringourfl ... d-annelida

All of these are protostomes, not deuterostomes. We differ from protostomes in the way the mouth and anus form in the blastula during embyrogenesis. The existence of myotomes and a notochord clearly show that Pikea is a chordate, not a worm. (Let me know if I'm moving too fast for you).

But those laws of chemistry and mutability and so on, like a Rubik's cube's laws of legal possible manipulations, could also have such behavior that they too make certain outcomes impossible - you merrily assume this cannot happen.

Well, that's a testable assumption. Show me one gene that could not have been produced by mutation of a different gene.

My dear fellow, I have not asserted that the human genome cannot be reached from a prehistoric worm genome,

That was a separate error on your part. See above. But you've now retreated to admitting that there is no proof against common descent? We're making progress.

The error is entirely yours, you claim humans did evolve from worms (see above) and your argument for that is that we have no proof that they cannot.

Nope. My argument is that the evidence, such as the variations in cytochrome c, clearly show that all organisms on Earth are of a common descent. As you now realize, the variations in that enzyme sort out in the same phylogenies we get by fossil transitionals, DNA analysis, and other evidence. You know this; everyone here knows I've shown you this. Why bother saying otherwise?

As you are now learning he who states a proposition carries the burden of proof for supporting it

Which, I suppose, is why you don't want to talk about the way variations in cytochrome C sort out. As you see, it fits an evolutionary model precisely, but it's completely incomprehensible to creationists.

and you have offered no proof that the Pikaia genome can ever develop into the human genome under the influence of just natural forces and time

I showed you that even for worms (which Pikaia is not) the differences in cytochrome C are entirely natural mutations that we see happening every day. There's really no point in you denying the fact.

As a simple example from group theory (exemplified in this case by a Rubik's cube whose legal conformations from a group) shows, in some cases not all conceivable conformations can be reached from some other conformation using just the rules of permutation for the group.

If so, it should be simple for you to show us any gene in a human that could not have formed by mutations. What do you have? By all means show us your calculations from "group theory" to support your claim.

And as you just learned, the structure of cytochrome C shows evolutionary connections between humans and nematodes. And as you now realize, the difference in the two forms of cytochrome C are those that are caused by processes which observably happen in nature. These different sorts of mutations are being constantly observed, so we have proof of the way these changes happen. But it's better than that...

We can get a phylogeny from the different forms of cytochrome C in different taxa, which gives us the same phylogeny as obtained by DNA, the fossil record, and other evidence...

Describing the difference between two configurations does not prove that one configuration is reachable from the other,

But showing that the differences are those that are the result of processes observed to happen, is compelling evidence for such evolution. As is this diagram, showing fewer differences between organisms with more recent common ancestors. Precisely what evolutionary theory predicts, but an impossible problem for creationism.

The "evolutionary connections between humans and nematodes" are inferred "connections" made on the assumption one evolved from the other!

No, that's a common logical error, though. The prediction was that the variation in DNA, enzymes and so on, between humans and nematodes should be greater than (for example) the differences between humans and rabbits. Turns out, that prediction was correct. Indeed, as you see, the variations produce the same phylogeny we see from other data.

There might be a host of reasons why structural similarities exist in nematode DNA and human DNA,

Occam would point out that the most reasonable cause would be common descent. For example humans and fruit flies share about 60 percent of functional genes. Chimps and human share about 96 percent of functional genes. And these nicely reflect the evolutionary distance between these species determined by other evidence. But if you have a testable hypothesis for some other reason, now would be the time to show us.

these can only be regarded as evidence for evolution if you can prove there's no other way for these similarities to arise,

Even many of your fellow creationists recognize the faulty thinking in that assumption. Kurt Wise, Todd Wood, Harold Coffin, and other YE creationsts who are honest and informed, admit that the evidence indicates evolution.

Your entire Rubik cube story is based on superficial, naïve extrapolation, just as would be the claim that the observed phylogeny of cytochrome C mutations were instead magically inserted rather than evolved.

Funny, quite revealing, how the very suggestion that such similarities might have a non evolutionary cause is simply incomprehensible to you.

There are lots of magical ways this could happen. The cytochrome Fairy, for example. Your problem is there isn't any evidence for that, and there is abundant evidence for common descent.

You hear hoofbeats and assume "unicorn", when you know horses are in the area. Logic isn't your strong point.

And the part you missed? You see every element in your Rubik cube is essential and locked into a very limited number of possible changes, while genes have much wider ranges of possible change.

Yes this is true,

But that's just the beginning. It's not going to help you to just chant "group theory" without showing us the math. And we both know that's not going to happen, don't we?

To assume that the genome we see in biological organisms is unrestricted is just an assumption.

As Darwin pointed out, it's not unrestricted. It's just much, much greater than you imagine.

If closure is present then evolution might not be possible,

As you now realize, it's directly observed. If "change in allele frequency" is confusing for you, use Darwin's term "descent with modification." Same thing, but you don't have to know anything about genetics.

But there's this, too; all cytochrome C molecules work the same way. How could there be so many changes without changing the function of the molecule? It turns out that most of the amino acids in a protein can be changed out in various ways without changing the function of the molecule. But a few regions where the activity is mediated, cannot change. So we have constant and variable regions of the molecule; the mutations happen in the variable regions.

This makes no sense, except in evolutionary terms. Which is something even James Tour should have realized, but for some reason, does not.

If the mutations are random why are they confined to regions at all?

They aren't. You've forgotten something else more than one of us has explained to you. Individuals don't evolve. Populations do. The reason you never see a mutation on a constant region of cytochrome C is simple. It would no longer function as cytochrome C in that case. And since it's an essential part of oxidative phosphorylation, no living thing on Earth could live without it. So those mutations just kill the individual, and we never see them in a population.

Once again, what you don't know, will hurt you. And it just did.