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I'm John Barry, am incredibly busy just now and plan to post a more detailed reply in the future-- if anyone still cares. However, let me respond briefly here.
First, I certainly know the difference between a retrovirus and other viruses, and I thank my critic for pointing out the imprecision of my language. In future printings of the book, this will be corrected. Any other factual error will also be corrected.
But most of his comments reflect either errors on his part, willful misreading of the book, or matters of opinion. Let me give you an example of each.
1. His error: He's wrong and I'm right about dendritic cells. Some, although not all, do do what the book says they do.
2. A willful misreading of the book: He complains about my sentence, "Antibodies, for example, carry thousands of receptors on their surface to recognize and bind to a target antigen." He argues that this means a single antibody can bind to thousands of antigens. Any reasonable reader of the sentence will conclude that it says the opposite. The antibody has thousands of receptors, but they only bind to one antigen.
3. Matters of opinion:... I think the evidence is very strong that the spring wave in 1918 was caused by the same virus as the second wave. But since the first wave was generally so mild, and killed so few-- the British Grand Fleet, which patrolled the coast of Europe, saw 10,313 cases but suffered only 4 deaths-- it's unlikely we'll ever get enough molecular evidence to prove or disprove this opinion. However, epidemiological evidence is in my opinion compelling.
There is no doubt a new pandemic virus erupted in the spring, long before late June when Taubenberger's article is willing concede that it began. In fact, the pandemic picked up its name "Spanish Influenza" when it struck Spain-- in May, before Taubenberger agrees that a pandemic existed.
So there are two possibilites. Either one pandemic virus was supplanted by another, or the same virus caused both waves. The first hypothesis is possible, and many people now fear that H1N1 could be supplanted by an H5N1 pandemc (or by a reassortant of H1 and H5, or another reassortant, or by an entirely different virus). But this seems quite unlikely.
More importantly, there is overwhelming evidence that spring wave exposure provided protection against the lethal wave. This protection was much greater than can be explained by the cross-protection that one strain might provide another. In fact it was equal to or better than a good modern vaccine. A modern vaccine is considered decent at 70% effectiveness, and a few years ago the vaccine was only 44% effetcive. Spring exposure protected against the fall wave often with 80-90% effectiveness. I wrote about this at length. See: Barry, JM, Viboud, C, Simonsen, L,, Cross Protection Between Successive Waves of the 1918-19 Influenza Pandemic: Epidemiological Evidence from US Army Camps and Britain, J Infect Dis. 2008 Nov 15;198(10):1427-34.
I wrote that article hoping to convince those who speculated that the waves were caused by different viruses that they were wrong. Apparently I was unsuccessful in this.
Those who argue the virus did not change virulence in 1918 are not being logical. They're being tautological. They are saying that influenza viruses don't change virulence; waves in 1918 were of different virulence; therefore the viruses were different.
Until H5N1 surfaced, most people did not believe influenza could jump directly from birds to people either.