229 replies to this topic

[John Schloendorn]

Hi all,
I am pleased to announce that thanks to recent progress, the need for soil donations has arisen once more.

Samples donated from now on will be used for:

- Culture-based screening against A2E (see page1).
- Metagenomic screening against oxysterol esters (other troublemakers in heart disease and stroke).
- Metagenomic screening against Alzheimer's protein beta-amyloid, which will be developed by our fine ImmInst director Justin here in Tempe.

Metagenomics involves the direct extraction of functional genes from environmental samples (rather than attempting to culture organisms). This has two advantages: First, it includes unculturable microbes, which some say account for up to 99% of all microbes. Second, the DNA samples can be copied, frozen down and stored indefinitely, which allows them to be used in the near and far future for other projets. So whatever you contribute now will become the foundation of a growing DNA library that will probably accompany us until the three LysoSENS targets (intracellular junk, extracellular junk, xlinks) are out of the way. In this first public offensive in the war on aging, the online life-extension community can truly make all the difference, by contributing their local microbial diversity. Show the scientific community how much you want to see aging defeated, by helping us make the most remarkable DNA library on this planet!

All types of environmental samples are suitable. Try to avoid sending whole plant and animal parts, since we are interested only in microbes. Otherwise, there is just one rule: Biodiversity is key.

For your convenience, here are the postal addresses again:

By regular mail:

John Schloendorn
The Biodesign Institute
PO Box 875701
Tempe, AZ 85287-5701
USA

(The above address cannot receive freight service)

By freight service:

K. Anderson / Schloendorn
The Biodesign Institute
1001 South McAllister Ave
Tempe, AZ 85287-5701
USA

(The above address cannot receive regular mail -- yes, it's true...)

Edited by elrond, 04 February 2008 - 06:57 PM.

[Live Forever]

John, I am sure these questions might be answered, but there are a ton of pages to this thread so I am just going to ask (and hope you don't get mad),

1) For mailing, by freight I assume you mean like UPS, FedEx, or DHL?
2) Any particular things we should look for as far as soil is concerned? (consistency, proximity to certain plants, etc?)
3) Is there a particular type of container that it should be shipped in?
4) Should we only ship one sample per package or ship more than one in each?

Ok, sorry. I have a couple spots in mind to get samples from.

[John Schloendorn]

Take it easy, even if they were asked before, which they aren't, I would be happy to answer them again, if I get soil for it ;-)

1) Yes
2) No. Try uniqueness to make your sample more valuable. Everyone will have a compost heap, not everyone will live next to a hot spring or go on holiday to the great barrier reef, if you know what I mean. This is more difficult if you're in the US, but for people overseas it will be easier to be unique thanks to their more unique location.
3) No. Leak proof would be good.
4) You can ship as many independent samples together as you want. You can put them in separate plastic bags or something, but we'll mix many of them anyway.

[ag24]

Hi everyone,

I want to emphasise the importance of John's push for diversity in soil samples. Don't do anything dangerous to get them, but bear in mind that any environment with an abundance of unusual organic compounds is likely to harbour microbes that can break those compounds down, and thus can probably also break down a variety of similar compounds. Since we have quite a few target compounds (things that accumulate in different tissues), the chances of striking lucky will not reach diminishing returns for a long while yet. John and Jacques are set up to test a wide range of samples in parallel and we're working hard to secure more funding to bring more manpower onto the project, so there is no danger of your sample being discarded because the researchers are swamped! The lysosomal enhancement project has begun extremely well in terms of enthusiasm from professors, students and funders alike (as well as donors of samples!), but it's a really ambitious and long project, so we can't afford to let it slow down (or even stop speeding up). Go for it!

[maestro949]

I just went and dug up about 15 various soil samples from my yard and the woods behind and will drop them in the mail today. As a gardener I order a lot of plants from nurseries that usually come with soil from their area (or commercial potting soil - not sure if those are a problem, usually just soil, peat and pellets with nitrogen etc). Several of these soils are included as are some from under a bat house, slime mold infested soil, some from under some rotting vegetation, soils supporting mushrooms and some mud from a nearby swamp.

[John Schloendorn]

Glorious, thanks guys, I can't wait to get my hands dirty ;-)

[Live Forever]

Made a blog post about it at Betterhumans (direct link to it), so maybe that will help a bit. Hopefully you don't mind John, I copied and pasted your text, and added a bit of commentary. (I didn't figure you would sue me for plagiarism, [sfty] , seeing as how I don't have any money)

[maestro949]

Some microbe / soil facts from various websites...

- Microbes and their communities make up the foundation of the biosphere and sustain all life on earth.
- 99 percent of all these creatures still lie beyond the reach of science; they are unidentified, and their biological riches remain untapped which means most of the current generation of antibiotics came from just one percent of all soil-based organisms
- It is estimated that there are a billion times more microbes on Earth than there are stars in the universe � an estimated nonillion (one followed by thirty zeroes) microbes.
- A gram of soil can contain 2,000 to 3,000 different species (not different microbes but different species!) of microbes yet we have only described about 5,700 species. Amazingly, the total mass of all of these invisible creatures exceeds the mass of all plant or animal life on Earth, yet they are largely invisible to us.
- Inside the gut of one worm there are ten times more bacteria, enzymes and microbes than there are people on the planet.
- Fertile soil has about 5-million microbes per gram.
- Soil microbes recycle nutrients in organic materials back into forms useable by plants and other microbes.
- The Principle of Microbial Infallibility states that for every naturally occurring organic compound there is a microbe or enzyme system that can degrade it.

[estropico]

Hi there, I've advertised your request for soil donations on the UK list ExtroBritannia. Here's the message (mostly copied & pasted from this thread):

http://groups.yahoo....essage/2028?l=1

Give me a while (for the translation) and I will send a similar message to my Italian language list (http://groups.yahoo....group/estropico)

I plan to collect at least a couple of samples in the next week or so - hope I'll manage to encourage others on the above lists to contribute too!

Keep up the good work,
Fabio

[maestro949]

I tried posting to a gardening forum that I'm part of but the moderator nuked it. He's a bit anal. A few weeks ago he PM'ed me to tell me that he changed one of my posts that read "damn" to "darn." Moral of the story, make darn sure you get permission or aren't violating the darn MB rules.

[jaydfox]

Neat, Check it out:
http://science.slash...6/06/15/1216214
which points to:
http://www.fightagin...ives/000878.php

Looks like Reason at Fight Aging managed to get this posted on Slashdot!

[jaydfox]

One of the funding organizers notes: 'We're working hard to secure more funding to bring more manpower onto the project, so there is no danger of your sample being discarded because the researchers are swamped!'"

Unless the researchers get slashdotted with dirt samples... hehe...

[reason]

Sadly it wasn't on the main index, so not much traffic. But you could all go digg this:

http://www.digg.com/...ng_Life_Science

[Anne]

I notice that one of the Slashdotter's comments was basically mocking the fightaging.org main page -- um, maybe if he'd taken the time to, you know, *read the content*, he'd have gotten a better impression. It's true that there's a lot of quackery and pseudoscience out there, but not everything related to aging research is automatically pseudoscience by virtue of its subject matter. Being a mindless pessimist is just as bad as being a mindless optimist -- it's the "mindless" part that stands out here.

I'm in Northern CA and will be looking for interesting dirt this weekend...if I can figure out the postal logistics, I'll try to have some dirt on the way soon.

[John Schloendorn]

Ahh hi everyone, and thanks for your support! However, I need to issue a warning:

Please be aware that too much publicity for such an early stage project as this can be harmful. In particular, before we can involve the media or large numbers of people, there needs to be at least one, better more, scientific publications out. As long as there is little data to back up Aubrey's claims, the project will remain powered by immortalists visionaries alone. This is after all why I am doing this: I hope my results will enable the transition from a small philantropic adventure to a publicly supported large scale project. If we try to go public without the science to back it up, we
will have a soap bubble that will do more harm than good. Therefore, for now, let us keep the soil call private within the transhumanist community. After all we have members all over the globe with access to the neccessary biodiversity.

That said, I do not think a dangerous threshold of publicity has been crossed yet, but I do feel it might have come that far if I would not issue this warning. Sorry if this was a bit harsh.

On the bright side of things, I have setup a website for the soil call, aiming to put the information from this thread into a more coherent form

here

also announcing contest for the most creative environmental sample :-) Wherever you guys might have advertised this, please update your links to the web page. Maestro already offered to help with improving the web design, and I would like to extend this invitation to everyone. If you would like to volunteer to improve the design, add features ect, you are welcome to download the page, improve it at will and email it to me. If you wish to do so, it might be a good idea to post here and contact others like Maestro to avoid the frustration of duplicate efforts.

Fabio, and Liveforever, your outreach efforts to other transhumanist organizations are great, and I would encourage you to keep doing that. I am truly greatful if you could save me some time contacting other transhumanist webmasters to advertise the call.

[maestro949]

Good stuff John. I started chipping away at cleaning up the format and putting a menu on the page. I'll have something by the end of the weekend for review. If anyone has some graphics talent, I could use some help there for a banner across the top and interesting pictures that might be relevent. That test tube earlier in the thread isn't very appealing [huh].

$100? Perhaps we could take a collection and bump that up a bit. I'd be willing to throw some $ in. You might get more soil you can handle though if the turnout is anything like the other ongoing fundraiser

[jaydfox]

I'm sorry, I don't have time to read the whole page. You're German, so I assume the following was sarcasm?

And of course be sure to add some chocolate, packaged separately.

No offense on the German thing, I'd been to Germany a couple times in high school, and hosted German exchange students for a few weeks on a couple occassions as well, and I noticed they take their sarcasm very seriously, and mocked Americans for having to be so overt about our sarcasm. (You know, using that special sarcastic tone of voice, to cue the other person that what's being said isn't serious. The Germans I knew never used the tone, so it took a while to figure out when they were being sarcastic.)

[John Schloendorn]

the following was sarcasm

The following was the expression of an overwhelming craving for chocolate in a lonely night in a lonely lab. Can you imagine that only ONE soil donor so far was compassionate enough to actually respond and put in a delicious local chocolate bar? Anyway, thanks for pointing it out again, people tend to read over it.

using that special sarcastic tone of voice, to cue the other person that what's being said isn't serious

Yes, I strongly agree with your German friends, that's among the most ridiculous American idiosyncrasies :-)

[John Schloendorn]

Maestro hehe, good idea, make your pledge and I'll amend the text. Looking forward to your design.

[maestro949]

Here's a first crack at it. Don't use it yet though as it's just a prototype. I also pilfered the layout from somewhere else and want to "rework" the behind the scenes stuff so it's our own but it should give you an idea of where it's heading.

It needs a header and I was going to put some links to some of the science in the space to the left. If anyone else has any ideas feel free to toss 'em out.

[John Schloendorn]

rework" the behind the scenes stuff so it's our own

No idea what you're talking about, but I'm sure you know what you're doing :-)

Also, I just got your soil, many thanks! Can you please follow up with a brief declaration where the stuff is from, including your full name, by email is ok. I need these for proper lab log documentation, and also in case any ethics questions should arise.

[maestro949]

No idea what you're talking about, but I'm sure you know what you're doing :-)

I don't but I did stay at a Holiday Inn last night

Also, I just got your soil, many thanks!

Great. I hope the microbes enjoy their new home.

Can you please follow up with a brief declaration where the stuff is from, including your full name, by email is ok.

Done

I need these for proper lab log documentation, and also in case any ethics questions should arise.

*gulp* [:o]

[John Schloendorn]

*gulp*

No worries, nobody is going to bug you, your details will remain strictly confidential, but I have to be able to say with confidence that I can track the source of every sample that gets used in the research. If the soil donors wish, they get acknowledged on the mprize website here, and of course I ask everyone in personal communication if they're happy with that before I put their names online.

[maestro949]

Second, A2E is light-sensitive, so one would need a mechanism to let microbes in but keep almost any non-red light out

Luciferase is protein of the month at PDB that has bioluminescent properties. Maybe if you could get some of these enzymes into the Lysosome it would break the A2E down? According to wiki, potatoes have been engineered to produce the protein. Assuming it would even work you'd still have to figure out how to package up the luciferin, luciferase, deliver it and then find a way to trigger it to produce light. It looks like there are several molecular structures for luciferin.

My my darling. You have a nice glow to you.

Edited by maestro949, 17 June 2006 - 09:09 AM.

[John Schloendorn]

Very creative, and thanks for thinking, but unfortunately no... Photo-induced breakdown of A2E is one of the problems we want to avoid. Remember there's actually light shining into your eye all the time. And when it hit's A2E, the molecule will disintegrate, forming reactive epoxides and free radicals. For example, one of my collaborators pulled DNA out of these cells and found that A2E side chains were chemically bound to it, as a result of these photochemical reactions. They think that this may be one of the mechansims by which A2E deposits lead to macular degeneration. So we would like to find a more environmentally friendly, catalytic breakdown pathway that would for example result in things like water, co2 or vitaminA.

My my darling. You have a nice glow to you.

Yes, germline gene therapy is an interesting application, too ;-)

[maestro949]

Oh. Interesting. So does A2E only build up in the eyes or is that where your focus is? No pun intended.

You mention metagenomic screening. Is this related to directed evolution?

[maestro949]

Oh nevermind regarding the metagenomic screening. I answered my ? with this.

That's pretty cool though it looks like you'll be busy...

The scale of the task is not trivial- a gram of soil or litre of seawater contains many thousands of unique viral and prokaryotic genomes, hundreds of lower eukaryote species and DNA derived from higher eukaryotes [80,81]. Using conservative estimates of genome sizes [82,83], soil metagenomes may constitute between 20 and 2000 Gbp of DNA sequences.

[John Schloendorn]

Yes, A2E forms as a side-product of the normal visual cycle. Check out the medical bioremediation proposal, which is very revealing in this and other respects.

[John Schloendorn]

it looks like you'll be busy...

I won't deny that, but it also depends on how cleverly one designs their assays. If for example the design is so that only E.coli that obtained a gene for the desired activity will be able to grow in the assay medium, one can get around assaying those millions of clones individually. You would selectively amplify the type of gene you want in one pot, progressively diluting all other sequences out. Essentially one is limited only by the physical ability to construct clone libraries. This apporach has been somewhat unpouplar out there, because it discards the info how frequent your desired gene is in the environment. But with all these people dying out there, I tend not to be too interested in such "academic" questions.

Also, the particular quote you brought up is referring to metagenome sequencing, and that's of course completely different from what we're trying to do here.

[John Schloendorn]

Directed evolution is something I would be excited about, but we currently do not have the human resources to consider it.