No laugh here, but I bet this little amino acid has a lot to do with some of the function of the carbohydrate recognition domain. Here is a Pymol view of guinea pig SP-A from residue 51 to 347, rotated to show this AA. Someone out there knows exactly which on it is… i will try to find out. In addition, I will post the ferret sequence from the same location (also residue 51 to end) to see if there is a similarity. RED arrow points to the spike.
Modeling surfactant protein A has been a fun journey. Me, wellllll, this I had never done before last week. But I leaned by error that there is a FASTA statement that needs to be used in some programs. I guess I must not have typed this in correctly when I used the program at UMich either written by or run by Yang Zhang. FIND IT HERE: Yang Zhang. I-TASSER: Fully automated protein structure prediction in CASP8. Proteins, 77 (Suppl 9): 100-113, 2009. BUT in this case it incorporated my statement into the AA sequence, ha ha. and here you have what SURFACTANTPROTEINAGUINEAPIG looks like as a protein. The structure itself is wonderful, but the blue part at the bottom is the “monster end” read as an addendum “SURFACTANTPROTEINAGUINEAPIG” protein… ha ha… too cute, made me laugh. So just snip off the blue, and you have the real modeling of guinea pig surfactant protein A.
I googled erroneous diagrams in science and came up with a series of articles in Scientific American, but the link was broken. In case the repair the link here it is, but it seems that a paid subscription is necessary.
This blog just is another attempt to make individuals who write articles for scientific journals aware that they do a great disservice to our knowledge base when they carelessly use inaccurate and lazy renditions of data, just because they feel (or the editors feel) there should be visual content does not forgive “junk graphics”. If there is going to be visual content, then it needs to be accurate.
Scientific publications are not the place for “artistic” renditions unless they have basis in real fact. Artistic license is NOT an excuse for poorly made illustrations. I wont spend the time to detail errors in the diagram about which I am thinking at this moment, but it was so poorly drawn as to be laughable. An attempt to avoid asking permission for use of graphics from previously published works, or better diagrams from other publications, perhaps, or just trying to turn out another manuscript at warp speed, may have been the problem. I did in fact email the first author (who is at my same institution) and mention how sad it was to include “fake diagrams” in scientific works. I got a response but it was sadder still. Does the use of “fake diagrams” mean that there are “fake data” and “fake interpretations” in the publication as well. This all fits right in the “fake news” and “fake accomplishments” mentality rampant in our world.
What is even worse is that the reply from the lead author seemed to point to the idea that the bad diagram was justified by calling it “artistic”. This was an excuse, and it means to me that many in the scientific community think that “made up diagrams” are ok, even when good evidence says that what they “made up”, the depictions are erroneous. How egregious, especially when there is easy access diagrams with honest content of the same material.
It is a perplexing issue.