iiinova — where your digital self keeps evolving

Mark Pallen @mjpallen.bsky.social · 29/06/2025

tinyurl.com

The Essential Guide to Evolution: Amazon.co.uk: Pallen, Mark: 9798284529447: Books

Buy The Essential Guide to Evolution by Pallen, Mark (ISBN: 9798284529447) from Amazon's Book Store. Everyday low prices and free delivery on eligible orders.

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Mark Pallen @mjpallen.bsky.social · 17/01/2025

Well done! Their score of 345 trumps our highest score of 325 playing for @imperialcollegeldn.bsky.social in 1995-6 championship

Mark Pallen @mjpallen.bsky.social · 29/12/2024

Sad news. Jimmy Carter, former US president, dies aged 100 www.bbc.com/news/article... Frustrating that he didn’t live long enough to outlive the guinea worm. But nearly gone now thanks to him and a tremendous team. www.cartercenter.org/resources/pd... Donate here www.cartercenter.org

bbc.com

Jimmy Carter, oldest of all US presidents, dies aged 100

The Democrat served a single term as president, a late 1970s period of economic and diplomatic crises.

Mark Pallen @mjpallen.bsky.social · 28/12/2024

„Die gefährlichste Weltanschauung ist die derer, die die (mikrobielle) Welt nie angeschaut haben.“ Humboldt (fast)

Mark Pallen @mjpallen.bsky.social · 28/12/2024

Stimmt. Danke! Interessant, dass ihr critical thinking aus dem Englischen übernehmt, während wir Weltanschauung aus dem Deutschen übernehmen. 😉

Mark Pallen @mjpallen.bsky.social · 19/12/2024

@theguardian.com has eventually published an edited version of our letter. www.theguardian.com/science/2024... @pathogenomenick.bsky.social but behaved disingenuously in adding a title we didn’t agree to. There is *no* evidence of a brain microbiome.

theguardian.com

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Mark Pallen @mjpallen.bsky.social · 17/12/2024

@theguardian.com still not addressed its unbalanced reporting on non existent brain microbiome (failure of substance) but now presenting failure of style with regressive reversion to online offering aping printed version rather than built for mobile devises. 🤦🏻‍♂️

Mark Pallen @mjpallen.bsky.social · 14/12/2024

Not claiming that pathogens cannot enter brain but that there is no resident normal commensal complex microbial community in the human brain.

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Mark Pallen @mjpallen.bsky.social · 09/12/2024

@katharineviner.bsky.social please could you give us courtesy of a response to this letter? Or better still publish it in full and/or retract the unbalanced article to which it refers. I have been @theguardian.com reader all my adult life and it would be shame to have to break that habit over this!

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Mark Pallen @mjpallen.bsky.social · 04/12/2024

@theguardian.com Could your editor please engage in the courtesy of a reply to our letter sent to you yesterday on this misleading article? You can see it has generated much interest here on BlueSky, but should reach your entire readership if you care about balanced and accurate reporting.

A problem-based learning curriculum for the

I have injected AI generated Socratic dialogues into PhD student training. Eg mmbdtp.github.io/modules/meta... Students said they were surprised how polite such discussions were—even though AI generated they reflect the tone of the originals.

mmbdtp.github.io

MMB DTP Training

Well we didn’t get a transcript of all that was said between the two of them so choice of emotionally charged quote is nonetheless a choice particularly without balanced coverage. But will see what guardian editor makes of it. I expect revisions. But isn’t it nice to have reasonable discussion here?

And any discussion of debates in Guardian article is unbalanced. Calling people dinosaurs? Is that really permissible in balanced scholarly discourse?

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More clear I hope in revised version of the letter, where we refer specifically to the non-peer-revioewed study led by Lathe. Not sure whether by original article, you mean the Guardian piece or something referred to therein?

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Revisiting this old paper journals.asm.org/doi/pdf/10.1... which proposed the acronym YATM for "yet another typing method", might I suggest YALB1S pronounced yal-biss for "yet another low-biomass 16S study"?

journals.asm.org

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No. The Hu et al study that Lathe is senior author on.

The consensus microbiome paper is far less troubling in that the door should be open to accepting unrecognised or under-recognised roles for microbes in neurological disease. But that is different from accepting a resident commensal microbiome in health. Term "microbiome" muddies the waters here.

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Ah, we are talking at cross purposes. You are talking about the first paper cited, Lathe et al. and what you are seeing is the journal's copyright declaration. I was thinking about the Hu et al non-peer-reviewed preprint.

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Infection Medicine Awarded Benter Foundation Grant for Dementia Research

You mean the Benter Foundation? Looks like the money was awarded for something else and this study involved repurposing funding or resources rather than Benter specifically supporting it through grant review scheme www.ed.ac.uk/infection-me...

ed.ac.uk

Research on the association of viral infections with dementia has been given a boost by the Benter Foundation.

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I would have preferrred to cite Salter et al, but I don't think Guardian accepts scientific citations. But you are immortalised as the superhero of kitome science! What do you make of fish brain microbiome paper?

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NCBI Sequence Read Archive

Also an awful lot of salmon DNA in these supposed bacterial 16S libraries. See e.g. trace.ncbi.nlm.nih.gov/Traces/?view.... This brings to mind this paper suggesting another source of artefact. microbiomejournal.biomedcentral.com/articles/10....

trace.ncbi.nlm.nih.gov

SRA Archive: NCBI

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Flavobacterium psychrophilum - Wikipedia

And seeing a few bacteria doesn't mean that there is a complex resident microbial community there in the brain. Could just be infection. Note that there are pathogens in at least some of their samples. en.wikipedia.org/wiki/Flavoba...

en.wikipedia.org

Visualisation of bacteria by confocal mildy convincing, but need to know precisely what they are. Why no attemot to visualise via EM?

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Look at this telling comment: "A total of 54 isolates were recovered from different trout brain regions and different animals (table S1) and 120 isolates were obtained from all tissues sampled." Dont tell us what the 120 were nor ifthey appear in 16S data. Null hypothesis: contamination predominates

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Key point is why bother with underpowered 16S studies. Most of what they say they see in 16S could be cultured, so why hasnt it appeared in the cultures? Need to see clear comparison of 16S stuff that should be culturable and actually was cultured.

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So, your article much more balanced than others we have seen, which is good. Fish study better than those mentioned in guardian article, but still open to doubt or at least more conservative interpretation.

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in print version I am afraid. I first heard of chloroplast sequences in 16S studies of sterile sample from human knees >20 years ago. Same old errors.

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updated version of letter to the guardian in reponse to word limit.

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Mark Pallen @mjpallen.bsky.social · 02/12/2024

Letter sent in to the Editor of the Guardian on brain microbiome nonsense.

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Thanks for this. As noted concentrating on guardian article for next day or two and have only skim read yours but will get in touch later in week. And allow me to say how refreshing your approach is!