That is the objectively correct way of defining “fitness”. You and your creationist colleagues just try to reject it because it does not allow you to make the claims you want to make.
That argument only works if you use a subjective and non-rigorous definition of “damaged” and “more robust” that can be changed to produce whatever result you wish. This is what you and your creationist colleagues are doing, and is why your argument is fallacious.
The purpose of the experiment described in that paper was to test that claim. What did they find?
Because they are different diseases, caused by different strains of the flu virus. These strains arise, among other means, by re-assortments of the various RNA genome segments that constitute the viral genome.
You need to take a close look at those viruses. Download their genomes and do a BLAST search and show where they have pig or bird DNA in them. The pig or bird genome doesn’t contribute to the genetic information of a new viral strain. A “new” viral strain such as the swine flu results from the recombination of two previous strains of virus inside a pig but does not include the pig DNA itself.
With all this talk of mutation and genetic entropy, may I pose a question which has been rattling about for some time? When I hear of mutation, my reflex is to think of a base pair substitution which leads to an altered protein. However, it seems to me that most differences in closely related animals are due to gene expression leading to different morphology. Is it true the biggest difference between wolves and mountain lions is developmental biology, not that they are made of different proteins?
So my genetic expert friends, for my education, is gene expression or base pair substitution for coding DNA the principle driver of adaptation, or is this a naive distinction to begin with?
Which brings us back to the matter of the figure you cite. In actuality, there is no extinction of viruses, just evolution. Which does not seem to jibe with your use of the figure.
I asked Dr. Carter the same thing. This is very interesting and complicated, but his layman-level explanation was (and this is my fallible paraphrase) “These viruses are relatively inactive and benign (perhaps even symbiotic?) in their respective animal hosts, but when they jump to humans they burn fast and hot.”
Mutations are heritable changes in DNA sequence, and this applies to all parts of the genome. If mutations occur in a transcription factor of promoter then they can affect gene expression.
That’s a tough one to answer because the function of a protein can alter the gene expression of many other genes. Mutations other than substitutions also play an important role, such as recombination mutations that can duplicate genes or put a new promoter in front of a gene. Biology is rarely black and white, and this certainly applies to evolution.
That’s a question I don’t have an answer for. It was my understanding that the mutation rates in the benign state (in the animal host) were not as high as in the pathogenic state. If that is not true, then I personally don’t know the answer. Dr. Carter might, but I know this is a very mysterious topic where more research is needed.
EDIT:
I should have realized this, but Dr Carter did already address this question in the box at the bottom of creation.com/fitness (he wrote that box part!); he is saying that the waterfowl apparently have regulatory mechanisms in place to maintain the integrity of the virus, which is beneficial for them.
As I said to Dr Swamidass, it was my understanding that in the benign state they were not mutating as much, though I don’t understand all the reasons. This is an interesting topic for sure.
EDIT:
I should have realized this, but Dr Carter did already address this question in the box at the bottom of creation.com/fitness (he wrote that box part!); he is saying that the waterfowl apparently have regulatory mechanisms in place to maintain the integrity of the virus, which is beneficial for them.
A whole lot is known about flu viruses, replication in different hosts, mutation and reassortment, etc. etc. These matters may be mysteries to Dr. Carter, but not to the flu virus community.
@Mercer’s head is going to fairly explode, I fear …
I’m conversing with YOU, Paul, and trying in good faith to correct YOUR misunderstandings. That was an evasion.
Have you looked?
Will you swear on a Bible that you look into the primary literature on DI particles?
I’m not seeing any curiosity. I’m just seeing a frantic attempt to deflect and obfuscate.
Because the authors are not only looking at FIXED mutations, as what was in the graph you grossly misrepresented and promised to correct. You don’t know what you are talking about; you are only looking for language that you can twist to win, and you’re not looking at evidence.
[quote=“PDPrice, post:53, topic:8253”]
Mercer: More importantly, the virus never became extinct. If you disagree, please explain how you think they measured extinction.
Carter and Sanford wrote: “We provided data that more than suggests that the various influenza viruses that infect humans cannot survive long term, and we were the first to notice the disappearance of the human version of the H1N1 influenza virus in mid-2009.”
Note that they didn’t use the terms “subtype” or “strain.”
Why does the CDC show an arrow extending to the present day?
If the H1N1 subtype went extinct in 2009, how do you explain all of the following outbreaks?
Given that you clearly don’t even understand the virology on the most basic, Wikipedia level, it is very difficult to see your response as anything but naked deception, Paul. The fact that you may deceiving yourself first in the process does not excuse misinforming innocent people.
Your spreading of misinformation in this matter, deliberate or not, has the potential to kill people if they take your uninformed opinion over the CDC’s. You have an ethical obligation to know what you are writing about.
That is, very clearly, not what they are talking about in their paper, and the CDC graph I posted also makes it abundantly clear what they were talking about. (Spanish Flu only)