16 replies to this topic

[John Schloendorn]

Hi fellow grad students,
Like some of you that I ran into on ImmInst, I’m currently looking for a position to do a PhD. That is, of course, I want to end up somewhere really, really productive in terms of life extension. Now I see that some universities and labs encourage the submission of proposals for PhD projects by the prospective students. So I’m planning to write one or two such proposals as I get the chance, just to have something at hand to rub under anyone's nose who might offer me an opportunity.
If you are in a similar situation, maybe we can exchange such proposals for “peer review”, or advise each other in the writing? If you’re interested, be sure to post your thoughts.

[olaf.larsson]

Which area are you going in to?

[John Schloendorn]

Can't decide :-) I think stem cell therapies / tissue engineering is something we will certainly not get around.
But in the short term, it may be more useful to try and change public attitudes with the creation of transgenic mice with slow aging or reduced cancer. In this category one could go for nearly any SENS, such as lysosomal enhancement, extracellular matrix treatment, DNA repair, suicide genes vs cancer...
Furthermore, I am thinking about direct somatic cell gene therapy to save the neurons.
What do you think?

[olaf.larsson]

We need need..

1)Whole Body Gene Theraphy. From reading here you could get the impression that we allready have it but we dont.

2)Systems biology modeling i computers to understand what to change and how to change it. I think its sounds as a better aproach than endless experiments with transgenic mice.

[John Schloendorn]

1) If "gene therapy" includes cell replacement therapy with in-vitro engineered stem cells, then we fully agree on 1.
Although cell replacement therapy has the advantage that it might rejuvenate in its own right, simply by replacing old cells with young ones, without the need to know or tamper with the genetic, intracellular causes and mechanisms of aging.
In researching stem cell reseeding / tissue engineering, I would thus further both whole body gene therapy, and cell therapy in its own right.

2) I don't think systems biology is at a point where it can evolve on its own, unbacked by experimental data. Apart from that, no one is going to rush to fund aging research when we can make an immortal mouse in the computer. But it's not really my field, so keep trying to talk me into it!

[olaf.larsson]

To make a transgenic mouse in the computer cost nothing once the models are worked out. To make a transgenic mouse in real world will always cost much time and money. Once you have a good computer model of a good antiaging intervention, you practicly have it in real life also, if you asume that the model is correct. In conventional lifescience research 99% of the money and time goes to experiments that fail, to work out and find the method that will work. But once good computer models are made there will be no more failures, similar to as you don´t build prototypes of airplanes anymore this days. But cells and organisms are more complicated than airplanes so it will take more time to work out this models.Yes systems biology ofcourse needs microarray experiments, and antibody arrays would be good, they are in experimental state right now I think. Yes I know that most biologists dont like computers very much, but at least some of us must go into computer science. Even if I love all this beautyfull proteins, the number of diffrent interactions gives me headic, and I would love to be able to model them and see them in front of me what is acctually going on without any simplifications. The joy to be able to do this will be much greater than pain of learning some programing and computer science.

[John Schloendorn]

Hmm, sounds ambitious. But who would be scared of ambitious projects, around here :-) It's certainly good to see that all this is happening.

But I'm one of those biologists that don't like computers very much, so I'll give it another shot:
Don't you think all this beautiful computer stuff is happening anyways, I mean, no matter what we do? Most biologists on earth are busy generating the data to feed in those computers, and as a consequence, the effort, money and genius put into the development of these programs should already be big. Good people are willing and able to do this in my place.

That can't be said of making transgenic mice with the explicit purpose of longevity. It also can't be said of stem cell therapies to fight aging, rather than any specific disease. I want to go into a field where I can make a difference, or I could as well drop on the beach and slurp pina coladas until the work gets done.

My immortalist motivation is the only thing that sets me apart from zillions of other grad students out there. Thus, in order to make a difference, I want to do those jobs that no one else has the motivation to do.

[caliban]

My immortalist motivation is the only thing that sets me apart from zillions of other grad students out there. Thus, in order to make a difference, I want to do those jobs that no one else has the motivation to do.

If your own project plan does not bear fruit, I think Mondey could be tempted to take you up in this. )

[John Schloendorn]

Hope so. Lets see how our little collaboration is going [thumb]

[John Schloendorn]

Assuming that I could contribute at least a tiny little bit to the extension of even your life span, it becomes automatically your peril. So you should talk me into it, as if your life depended on it!
Btw, I'm not thinking about ignoring it, but merely about having its fruit while someone else waters its tree.

[ddhewitt]

Even though systems biology holds much promise, I am not going to hold my breath.

I think there is much real world experimentation to be done before sophisticated computer modelling of biological systems becomes a reality. Hopefully I am being too pessimistic.

Duane

[manofsan]

I'll agree with you, but lab-on-chip devices and further automation will allow the entire metabolic network to be mapped. The VLSI of metabolic chemistry can then be modelled and simulated, just like a microchip can be.

We will then be able to computationally derive phenotype from genotype, and vice-versa, through purely numerical methods. Hey, if 3D render software can create an entire scene from limited geometry data, why can't we one day have the physical image of an entire organism being rendered from just the DNA sequence code? I believe it will one day be possible.

Comments?

[John Schloendorn]

One day, certainly, for we all have seen Kurzweil's computer power progress curves [tung]
As far as I'm concerned I'm planning to live forever here, and I think sticking with empirical evidence, i.e. science, is a good way to do that. Sure thing, it's nice to predict what happens to my chips with a chip, I just don't see how this is relevant for our present race against time here.
Aubrey once wrote that you don't have to know anything about how a horse works to make it carry you where you want to go. I would agree with him that we are having a situation here, with aging and death and the likes, which does not permit us to take the time to find out all the details of how it works, even though that might be somewhat helpful.

[olaf.larsson]

To model ALL interactions in a biological system like a human may seem a daunting task to say at least. We are in the same possition as if someone would say to us in 1975 that we are going to map the whole human genome, when the latest thing in sequencing is that phage phi X-174 has been mapped.
I see in front of me standarised high troughput screening methods, antibody chips etc. diffrent labs can offcourse work with diffrent parts of the Net of interactions. You dont need a model with every detail correct to be able to use it.

John, Before I didn´t like computers much eighter, thinking of working with computers made me sick. I guess that the I strated to like computers more when I attended a bioinformatics course. Then I saw biology pure, beautyfull, logical, possible to overlook. Not slimy, wet, frustrating and timeconsuming as it could be in the lab.

Here is a book about systems biology it looks wonderfull at least from outside:

http://www.amazon.co...=books&n=507846

Dont the networks of interactions make you frustrated? The psycological pain and frustration with beeing unable to overlook the networks of protein interactions makes me to work with computers becouse I look forward to the day when I can see the interactions pure and clear.

Edited by wolfram, 13 January 2005 - 08:09 AM.

[John Schloendorn]

Yep, right, grad student. A gel a day keeps the reaper away. That is, if you don't spill the dye over your fingers. A few days ago I prepared a gel to settle over night, and no kidding, found a huge crockroach on top of it the next morning. When I tried to grab it, it shit on my gel and vanished under a cupboard. Today I found it upsidedown in a corner, dead. I wonder how these guys want to survive a nuclear war when they can't stand a few microliters of ethidiumbromide...

Thanks guys for the infos, I'll definitely try to get a hold of that book.