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Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

nature.com

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Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#111

Post by troymc »

dynomight wrote: post #108
dynomight wrote: post #107

Earlier quoted context omitted.

This may be sloppy science, but sometimes discoveries happen in very sloppy and unpredictable ways.

Excuse me. Science only happens in precise and predictable ways.

Scientific discovery often happens by accident, i.e. unpredictably. And when you're not expecting to discover something, you're obviously not being precise about it.

A concrete example is the accidental discovery of the cosmic microwave background radiation. If you Google "accidental discovery" you'll find hundreds of other examples.

Or, if you prefer an Asimov quote:

"The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...'"

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#113

Post by sooheon »

TeMPOraL wrote: post #104
nonbel wrote: post #83

Nature is not a good scientific journal. The good info will be found in highly specialized journals. The amount of BS in scientific journals is related to prestige like this: x=seq(0,1,by=.01); plot(x,dbeta(x,.5,.5), xlab="Prestige", ylab="BS")

For those without a R interpreter handy, Emacs to the rescue: ^ | | | | | | | | | | | | | \ / | | | | \ / | | | | \ / | \ / | \ / B | \ / S | \ / | -\ /- | \ / | -\ /- | -\ /- | --\ /-- | --\ /-- | ---\ /--- | -----\ /----- | ----------------- | +---------------------------------------------------------------------------------> Prestige (Also an on-line R interpreter: http://www.r-fiddle.org/. )

What package(s) did you use to create this?

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#114

Post by cstross »

solofounder7 wrote: post #84
et2o wrote: post #63

Earlier quoted context omitted.

It's known to be pretty difficult to treat a lot of fungal infections in the CNS. The agents we have are pretty nasty, with severe side effects.

I'm a hacker not a doctor but I've done some research into water purification, and here is what I've learned: The body is mostly water. The task of removing microorganisms and fungus from water has been well studied. Science knows of effective agents which are proven to purify water of micro-organisms like bacteria and also fungus. Some of these are being utilized in public water decontamination, and others while als…

"Airliners are mostly aluminum. Aluminum has well-understood properties, including flight. So if an airliner stops flying we can fix it by filtering out whatever impurity was responsible."

Sounds nonsensical to you? Good. Because that's about how reasonable your "the body is mostly water" thesis sounds to someone with a biomedical background.

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#115

Post by twic »

nonbel wrote: post #99
dnautics wrote: post #97

Earlier quoted context omitted.

Yeah, but that's true for monoclonals too, just a matter of degree. A polyclonal antibody is an extraction of (usually rabbit) blood from an animal that has been insulted with the agent you'd like to detect. The extraction is enriched for antibodies. They are less reliable, because there could also be other antibodies in there. Even the antibodies that recognize what you're looking for could be a population of antibo…

>"you can be confident that a monoclonal antibody contains only one antibody, that recognizes only one antigen" Not sure if you really meant that since it is kind of contradicted by some later statements, but all antibodies are promiscuous. Thinking you can map one antibody to one epitope is extremely dangerous. It is a matter of quantity (affinity/avidity), not quality.

Exactly. When i did immunocytochemistry, i had more confidence in polyclonals than monoclonals. If you get a strong signal with a polyclonal, then you know that many different antibodies are all binding the same thing, so it's very likely it's your protein. If you get a strong signal with a monoclonal, that's just one antibody - so it might be your protein, or it might be some other protein that, by chance, your antibody happens to bind tightly.

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#117

Post by seesomesense »

solofounder7 wrote: post #84
et2o wrote: post #63

Earlier quoted context omitted.

It's known to be pretty difficult to treat a lot of fungal infections in the CNS. The agents we have are pretty nasty, with severe side effects.

I'm a hacker not a doctor but I've done some research into water purification, and here is what I've learned: The body is mostly water. The task of removing microorganisms and fungus from water has been well studied. Science knows of effective agents which are proven to purify water of micro-organisms like bacteria and also fungus. Some of these are being utilized in public water decontamination, and others while als…

Eat a kilogram of potassium iodide and see what happens.

SPOILER: . . . . . You will die of hyperkalaemia

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#118

Post by twic »

dnautics wrote: post #97
moyix wrote: post #79

Earlier quoted context omitted.

Could you elaborate on what polyclonal means here? Does it mean that they might not have detected fungus after all, but some other thing that would activate the same antibodies?

Yeah, but that's true for monoclonals too, just a matter of degree. A polyclonal antibody is an extraction of (usually rabbit) blood from an animal that has been insulted with the agent you'd like to detect. The extraction is enriched for antibodies. They are less reliable, because there could also be other antibodies in there. Even the antibodies that recognize what you're looking for could be a population of antibo…

It might be worth explaining a bit more about how antibodies are made. There are these cells called B lymphocytes, whose job is to produce antibodies. When they form, they randomise parts of the antibody genes:

https://en.wikipedia.org/wiki/V%28D%29J_recombination

As a result, every B lymphocyte makes one particular antibody that is different to every other B lymphocyte, and which recognises a different molecular pattern to every other B lymphocyte. There's a process in their development which weeds out cells which recognises patterns in your own body, leaving a population of cells which (hopefully) recognise every possible pattern which is not part of your own body.

B lymphocytes then wander round the body, looking for stuff which binds to their antibody; if they find it, they know it must be an invader, and they raise the alarm, triggering an immune response (subject to checks and balances from other parts of the immune system). As part of that, the cell which raised the alarm will proliferate, making millions of cells producing identical antibodies, which bind to the invader and mark it for destruction by other cells of the immune system.

If an invader has more than one molecular pattern (which it will - every patch on the surface of a protein is a pattern, and a bacterium will have all sorts of proteins and other things on its surface), then a corresponding number of B lymphocytes should recognise it, and proliferate in response.

So, if you insult a rabbit with your protein, you will activate all the B lymphocytes which recognise patterns on it. If you purify antibodies from its bloodstream, you will get antibodies recognising all those patterns - and any other antibodies which happen to be in the bloodstream at the time. If you isolate a single B lymphocyte its bloodstream, make it immortal, culture it, and purify the antibodies from that, you will get a single kind of antibody, recognising a single molecular pattern.

In software terms, a monoclonal is a bit like detecting spam by grepping for a single spam-specific word, and a polyclonal is a bit like doing an n-gram comparison with a corpus of known spam.

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#119

Post by amelius »

troymc wrote: post #111
dynomight wrote: post #108

Earlier quoted context omitted.

Excuse me. Science only happens in precise and predictable ways.

Scientific discovery often happens by accident, i.e. unpredictably. And when you're not expecting to discover something, you're obviously not being precise about it. A concrete example is the accidental discovery of the cosmic microwave background radiation. If you Google "accidental discovery" you'll find hundreds of other examples. Or, if you prefer an Asimov quote: "The most exciting phrase to hear in science, the…

I think that even the "Eureka!" type of discoveries may be labeled as accidental.

Re: Different Brain Regions Are Infected with Fungi in Alzheimer’s Disease

#120

Post by zeckalpha »

3327 wrote: post #22
modeless wrote: post #19

All of the Alzheimer's patients were 79 or older, while all of the control patients were younger than 79 except for one. More than half of the control patients were under 60. That doesn't seem like a very good control to me.

Perhaps but the discovery is still significant. Until now there was no such correlation with Alzeimher's and Fungi. This has significant implications in terms of direction of future research.

The improper control means that there is a just as strong of a correlation between age and fungi.
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