Are 68 Molecules Enough To Understand Diseases?

Roland Piquepaille writes "A researcher from the University of California at San Diego (UCSD) claims that 68 molecules can explain the origins of many serious diseases. After reviewing findings from multiple disciplines, he 'realized that only 68 molecular building blocks are used to construct these four fundamental components of cells: the nucleic acids (DNA and RNA), proteins, glycans and lipids,' and he said that 'these 68 building blocks provide the structural basis for the molecular choreography that constitutes the entire life of a cell.'"

Comments

Overkill

[Tubal-Cain]

You should only need 42.

So.....

[RollinDutchMasters]

He's just discovered something that's in every first-year biochemistry textbook that's been published for the last 30 years?

I love when 'cutting-edge research' is actually old information with a pretty new graph/picture/powerpoint slide/animation/etc.

Re:So.....

[gnick]

You have to admit, it is an awfully pretty picture: http://ucsdnews.ucsd.edu/graphics/images/2008/09-08MolecularBuildingBlocksBIG.jpg

And I thought the write-up was fine. TFS focused on the '68 molecules' thing, which is nothing new. TFA just mentions that his research includes the illustration, but the thrust seems to be encouraging a focus on lipid and glycan research for disease control and steering away from our current tunnel vision of genetic research. Seems like a reasonable and interesting opinion considering that the lion's share of funding is going to the genetic researchers.

Are 2 Bits Enough To Understand Computers?

[Anonymous Coward]

An AC on Slashdot claims that 2 bits can explain the origins of many serious computer viruses. After reviewing findings from multiple hosts, he 'realized that only 2 bits are used to construct these four fundamental components of computers: the processor (x86 and x86_64), memory, storage and network tubes,' and he said that 'these 2 building blocks provide the structural basis for the bitwise choreography that constitutes the entire life of a computer.

Re:Are 2 Bits Enough To Understand Computers?

[Ethanol-fueled]

I've had enough of ACs' two-bit advice. Here's a quarter -- go call somebody who gives a shit.

Nah, just kidding man. Mod parent insightful.

Re:How many were you expecting?

[jellomizer]

And wow most of those Molecules are made up of Carbon. Without Carbon we will have no Diseases.
Sometimes going to deep in the problem causes you to overlook the obvious. For most Diseases it is about understanding how the elements function more then what they are made up of. (Sometimes knowing what they are made up help understand their function, but not always it depends on how they are arranged, just as DNA has the same molecules from one life form to an other their effect on the environment depending on their arrangement varies.

Obvious and boring

[Cougem]

How did this make slashdot? I have so many complaints with this

1. It's obvious - since these are the only components in cells, and they have all been known for years, how is this remotely interesting?

2. It's not really relevant - It's like me saying "100 elements are enough to understand disease" - yes, all biological processes may only involve 100, probably fewer, elements, but how the hell does that aid our understanding? It's the identities and actions of the resulting molecules and macromolecular complexes, not their components, which define their actions

3. If we're going to be anal it is far fewer molecules - The 4 bases of DNA and the proteins involved in their replication are all we need really to understand all disease processes, for it is from this template, and the proteins which they code for, that everything comes from. These 68 are all coded for in the DNA, even the DNA itself. One may wish to be a bit more anal and include mitochondrial DNA and proteins separately, as they are a separate genome technically.

4. This is misleading. Not all constituents in the body are made from merely these building blocks. What about hydroxyapatite? This is an incredibly common molecule in our bones, but like so many other molecules in the body, it is a relatively simple organic molecule.


What a thoroughly boring and unenlightening piece.

Re:Obvious and boring

[OG]

1. It's obvious - since these are the only components in cells, and they have all been known for years, how is this remotely interesting?

It's interesting in that this is a nice summary of information that we've known for a while that has never been presented in so succinct a format.

2. It's not really relevant - It's like me saying "100 elements are enough to understand disease" - yes, all biological processes may only involve 100, probably fewer, elements, but how the hell does that aid our understanding? It's the identities and actions of the resulting molecules and macromolecular complexes, not their components, which define their actions

See below.

3. If we're going to be anal it is far fewer molecules - The 4 bases of DNA and the proteins involved in their replication are all we need really to understand all disease processes, for it is from this template, and the proteins which they code for, that everything comes from. These 68 are all coded for in the DNA, even the DNA itself. One may wish to be a bit more anal and include mitochondrial DNA and proteins separately, as they are a separate genome technically.

You either didn't read or understand the article correctly (and I suggest reading the original article in Nature Cell Biology; it's a very quick, high-level piece. As to your point, the molecules that compose RNA and DNA are only 8 of the building blocks he lists. The 20 amino acides that compose proteins (and the amino acids themselves are not encoded by DNA) make up another subgroup. Then you have your glycans and lipids as the other two main subgroups, again not encoded by DNA.

4. This is misleading. Not all constituents in the body are made from merely these building blocks. What about hydroxyapatite? This is an incredibly common molecule in our bones, but like so many other molecules in the body, it is a relatively simple organic molecule.

See above.

The whole point of Marth's paper is that there has been too much focus on genes and proteins as the origins of disease, and that the research into lipids and glycans that has been conducted hasn't been integrated well enough into the genetic research.

To that end, he put together a very nice chart listing the major constituents of a cell divided into four major groups, along with diagrams of where those molecules are found in the cell. His article is more of a commentary piece about how more integrative work needs to be done with a nice chart on how these pieces fit together. It's one I'll probably print out and hang on the wall, because I appreciate that it's simple and still conveys quite a bit of information.

Re:Obvious and boring

[OG]

Again, go back and look at the chart. He lists the 8 (not 5) nucleic acids involved in DNA and RNA:

Deoxyadenosine
Deoxycytidine,
Deoxyguanosine,
Deoxythymidine,
Adenosine,
Cytidine,
Guanosine,
Uridine

The first four nucleosides make up DNA, the last four RNA.

Re:Obvious and boring

[Anonymous Coward]

Well done. In a 2-line post you managed both be an ass-hole and make an ass of yourself.

* Applause *

Re:Obvious and boring

[philspear]

The whole point of Marth's paper is that there has been too much focus on genes and proteins as the origins of disease, and that the research into lipids and glycans that has been conducted hasn't been integrated well enough into the genetic research.

A large part of that is due not to researchers prefering genes and proteins over the others, but limitations in our tools for probing them. There is quite a bit of research into lipids membranes, but the field is having trouble agreeing on some of the very basic mechanisms due to technical limitations. It's much harder to replicate lipids than it is to do so for DNA or proteins. DNA sequences you can have as much as you want by tomorrow using bacteria or PCR. Proteins you can get a cell type of your choice to express it and then harvest it (this becomes more difficult with certain proteins like transmembrane ones and becomes much more difficult with protein complexes). Those come out very pure and have been exhaustively troubleshot. Lipid purification methods are less developed.

I'm no expert in that, but it seems like a vicious cycle of no one purifies lipids because there hasn't been much work done to come up with a cheap and fast way of purifying lipids because no one purifies lipids. If anyone knows of a way to purify lipids for as cheap as you can DNA, let me know.

Furthermore, you can manipulate DNA or proteins much easier than you can lipids. A professor was telling me once that there were only two people in the world who knew how to effectively modify lipids to do spin-spin labeling (I think that's a way of determining the orientation of two mollecules) and to buy purified modified lipids was outrageously expensive. In proteins on the other hand, it's my understanding that any grad student could make and purify protiens for spin-spin.

And lipid biologists are having trouble with the very basics of their field as a consequence of limited tools. Lipid rafts are potentially one of the most important functions of lipids in the bilayer, but it's quite controversial as to whether they exist or not. I personally am not convinced that they do. The evidence in support seems to all be artificial examples of where they could get certain lipids to self-associate, but real-life examples have as far as I know either not been sufficiently proven or have been disproven.

I don't mean to demean lipid biologists, that work is far above my head and it is definitely an area that is far, far underdeveloped compared to the genes and protein research that I do. My hat is off to them.

Basically, we're focused on genes and proteins because you work with what you can. When the tools for lipid studies catch up to DNA and protein, you can expect lipids to catch up.

Re:Obvious and boring

[Anonymous Coward]

This:

The whole point of Marth's paper is that there has been too much focus on genes and proteins as the origins of disease, and that the research into lipids and glycans that has been conducted hasn't been integrated well enough into the genetic research.

... is intelligent, reasonable, and bears repeating.

This:

A researcher from the University of California at San Diego (UCSD) claims that 68 molecules can explain the origins of many serious diseases.

... is vapidity on the order of "Engine make car go Broom!"

The key point of the paper is not that there are only 68 compounds which are important to understand disease, but that there are 68 basic chemical building blocks which are important to understand disease, and (here's the important bit) at this point we're really only looking at the interactions of 28 of them.

Re:Obligatory.

[krgallagher]

"68 should be enough for anyone."

When he tried for 69, he blew it.

Re:woo

[pesho]

117?! This is an overkill. I can boil them down to 3 subatomic particles - electron, proton and neutron. Physicists, feel free to pitch in. Lets get to the bottom of these pesky diseases.

Who submitted it? (was: Re:Obvious and boring)

[siglercm]

How did this make slashdot?

It was submitted by the Slashdot God of all Science Media, Roland Piquepaille, that's how.

Re:How many were you expecting?

[Kingrames]

This just in: Carbon-based vulnerability discovered in Carbon-based lifeforms.

Re:reductionism

[philspear]

Nonsense.

On a completely unrelated note, I've made an illustration with 5 essential parts of all buildings: nails, screws, wood, cement, and support beams. These 5 building blocks provide the structural basis for the architectural choreography that constitutes the entire structure of a building. These construction components may now hold the keys to uncovering the origins of many grievous architectural problems that continue to evade understanding.

Re:How many were you expecting?

[gnick]

Solution:
Ban carbon compounds.

Sure, it means losing one element and we'd have to give up a few things - I'm not saying we wouldn't get our hair mussed. But picture it - A world without disease. So which is better - A world with carbon compounds and rampant disease or a world where we give up carbon compounds and rid the planet of all disease? You decide.

=P

Re:woo

[LiquidHAL]

Strings. Science over.

Some Context

[OG]

This probably isn't a great article for Slashdot's front page. The original work referred to in the press release cited (and to be honest, the release overstates the original work to which it refers) is a piece of correspondence in a scientific journal of cell biology (Nature Cell Biology) from a cell biologist to fellow cell biologists calling for a more holistic approach to studying the origin of disease. It has a very specific target audience and a very specific message.

He states (correctly) that many people thought that decoding genetics would lead to understand the nature of disease, but that hasn't happened to the degree we thought it would. Rather, they (I'm not a cell biologist) need to look at the entire cell and all of the components of the cell, not just the genes and proteins.

To that end, he provides a very nice diagram that lists 4 major groups of organic molecules and shows at a high level how they fit together. It's a nice little reference piece for researchers and students and a nice reminder that the cell is a dynamic, complex body with many important components other than the genes and proteins that receive such a large amount of scrutiny.

Improved Summary

[SlashDotDotDot]

Researcher Proposes New Framework For Understanding Cells, Disease.

Researcher Jamey Marth, publishing recently in Nature Cell Biology, has organized 68 molecular building blocks into four categories and illustrated their roles within cells. Marth suggests that organizing these building blocks, much as chemists organize the periodic table, will "provide a conceptual framework for biology that has the potential to enhance education and research by promoting the integration of knowledge.". Roland Piquepaille and Thomas Joseph offer commentary on their blogs.

In other misrepresentations...

[Arthur Grumbine]

It has been discovered that there are only 3 elementary particles that are at the cause of ALL disease. We should be more focused on understanding protons, neutrons and electrons, then we could have ALL the answers, not just The Answer.

I mean, c'mon, there's only three of them, how difficult could it be?

Re:How many were you expecting?

[gnick]

Sorry for the self-reply, but I just realized the flaw in my logic and realized why my 'Ban carbon compounds' proposal won't fly...

There are carbon compounds in oil - No way the lobbyists are letting us get that through Washington... Oh well, I can dream.

Re:I've got 2 bits...

[bob_herrick]

I've got 2 bits, a 0 and 1, I can encode almost any piece of information in it. Even a 10 year old can understand 0 and 1!!! This stuff is easy.

Fixed it for ya!

Water

[mosb1000]

Somehow he seems to have missed water, which is crucial to all life processes as we know them.