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Monday, July 06, 2020

A storm of cytokines

Cytokines are a diverse groups of small signal proteins that act like hormones to turn on genes in blood cells and cells of the immune system. In COVID-19 the production of cytokines can be over-stimulated to produce a cytokine storm that activates immune cells producing all kinds of severe, sometimes lethal, effects. There are dozens of different cytokines but they all act in a similar manner. Each one binds to a receptor on the membrane of a target cell and this stimulates the cytoplasmic side of the receptor to activate a transcription factor that enters the nucleus and turns on a specific set of genes. The activation step requires phosphorylation just like dozens of other signalling pathways. (See Morris et al. (2018) for a recent review.)

I was curious about the structures of these cytokines so I looked up a few of them on PDB. Here are three fairly representative structures.



Morris, R., Kershaw, N.J., and Babon, J.J. (2018) The molecular details of cytokine signaling via the JAK/STAT pathway. Protein Science 27: 1984-2009. [doi: doi.org/10.1002/pro.3519]

13 comments :

  1. https://www.sciencedirect.com/science/article/pii/S0022519320302071?via%3Dihub

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    1. Texas Sharpshooter fallacy. The method advanced in that paper basically implies I can't have 10 consecutive ancestors, as the compounding improbability of the particular series of mutations I inherited is astronomically improbable. The paper is absolute crap.

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    2. One of the authors made it into Ronald Numbers' book Creationism in Europe:

      Organizing Scandinavian Antievolutionism
      ln the late 19705, Scandinavian creationists began to get organized. ln Sweden Förening for Biblisk Skapelsestro (Biblical Creation Society) was established, and in Norway in 1979 the young mathematician Steinar Thorvaldsen organized a three-day creationist conference at the Norwegian University of Science and Technology in Trondheim with the participation of Wilder-Smith, who was a frequent visitor in Norway at the time. Also the biochemist Duane T. Gish, a prominent member of the Institute of Creation Research, visited Norway. ln 1983 Bent Vogel and Peter Ohrstrom, two science graduates from Aarhus University in Denmark, and the arts graduate Ole Dichman launched the quarterly Origo as what was called "a scientific journal" and "an apologetic resource" for Protestants with evangelical leanings and an interest in natural science. The journal soon developed into a creationist society and expanded its activities to Norway. Steinar Tiorvaldsen, now associate professor at the College of Education in Tromso, joined the Origo staff in 1988, and in 1996 a Norwegian branch of the society was established with Peder A. Tyvand, professor of physics at the Agricultural University of Norway in Moss, as president. Now, editorial boards were organized in both Denmark and Norway, including academics with Lutheran, Pentecostal, and Adventist backgrounds.

      The other one co-authored rubbish with the Discovery Institute's own Ann Gauger:

      With their new article for the journal BIO-Complexity, University of Stockholm mathematician Ola Hössjer and Discovery Institute biologist Ann Gauger have set the standard for considering the question of a “first couple” in light of population genetics. Obviously, the possibility that human beings can all trace our ancestry back to such a pair would have profound implications.

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    3. "that paper basically implies I can't have 10 consecutive ancestors, as the compounding improbability of the particular series of mutations I inherited is astronomically improbable."

      I think that is actually not what the paper is about.

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    4. ST initiated the study, and OH developed the statistical model in Section 2.

      There is no statistical model in Section 2 -- just a general teaching presentation saying what some general statistical methods are, with no application of them in that section.

      The paper is a "laundry-list" of every argument creationists have made, accepting all of them. There is no new argument.

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  2. Anyone know what happened to Panda's Thumb?

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    1. Afaik a hard disk came to an untimely end. It is being restored and will be up again eventually.

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    2. Latest word is that it may or may not be a hard disk failure -- it may be some other hardware failure. Social distancing is slowing down the repair process. I can more authoritatively report that ways are also being explored of having the site served up elsewhere. All posts and comments have been safely preserved.

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    3. You can at least be assured that, since PT has been down for everybody, you haven't missed any dazzlingly good or groaningly bad posts or comments since then.

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    4. Yeah I wondered what happened to PT. last thing I dealt with was concepts on censorship etc and poof PT vanished. like it was censored! It wasn't as that is wrong from ideas of freedom of speech.

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    5. Who knows? A deity might have influenced the hardware failure.

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