I see…that you don’t see what you don’t want to see:
6. Allegations regarding the research into the H1N1 virus by Sanford and Carter
The problems with C&S’s 2012 H1N1 paper (A new look at an old virus: patterns of mutation accumulation in the human H1N1 influenza virus since 1918 - PubMed) are myriad. They claimed fitness declined, but didn’t measure fitness directly. The two proxies they used, virulence and codon bias, are completely inappropriate as measures of viral fitness. They ignored pandemic dynamics and the different selection pressures imposed by intrahost and interhost competition. They asserted with no evidence that the mutations they documented were responsible for the changes in virulence, and further asserted with no evidence that these mutations “attenuated” the virus in some way (i.e. disrupted its replication mechanisms in such a way that hampered its ability to reproduce). Oh, and for good measure, the virus they claim went extinct continues to circulate.
But putting all of that aside, here we’re talking about a different problem: That for the purposes of documenting mutation accumulation in the 1918-2009 H1N1 lineage, C&S used as a reference strain a 2009pdm H1N1 genome. “pdm” here stands for “pandemic”, as in the 2009 H1N1 pandemic.
The problem is that the 2009 pandemic H1N1 lineage was unrelated to the 1918 H1N1 lineage. They do not share common ancestry as H1N1 in humans. The 2009 strain was the result of reassortment between several swine and avian influenza strains and human H3N2. So the differences between the 2009 strain and the 1918 lineage are due to recombination, not point mutations. So you can’t just count all the differences and say “relative mutation count” – a huge chunk of those differences were from a different process, and in any event, you can’t just treat two different lineages as though they are a single lineage .
PCS show part of an alignment to defend their conduct, but actually illustrate the problem:
Here is a screen shot of one of the worst sections in the alignment. This is part of the hemagglutinin (HA) gene. Strains from 1918 through 1936 are shown. The human and swine H1N1 reference genomes are also there. We see one three-letter deletion (keeping the downstream codons in-frame) and many single-nucleotide changes. There is no evidence for large-scale rearrangements, either within or among the eight segments of the H1N1 genome.
Yes, because 1918 to 1936 reflects a single lineage, and nobody has said otherwise. The problem is the 2009 pandemic clade, which is distinct from the 1918 lineage. I’m not sure why PCS thought the above quoted paragraph would address that problem.
When you do this correctly, you actually have to detect and remove recombinant and reassorted sections from your genome alignments, so the recombination doesn’t mess with your mutation calculations. There are lots of ways to do that, but despite PCS saying everyone involved was well aware that reassortment occurred, they didn’t do anything about it! Just treated those differences like any other mutations, which…no! You can’t just do that.
So the mutation counts, a foundation of that paper, are wrong.
You were tagged in the first post and you participated in the second thread:
https://discourse.peacefulscience.org/t/stern-cardinale-response-to-price-carter-and-sanford-on-genetic-entropy
Why would it be interesting to discuss what someone said instead of discussing the actual facts that YECs deny?