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Are 68 Molecules Enough To Understand Diseases?

Posted by ScuttleMonkey on from the enter-the-peer-review dept.

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.'"

40 of 133 comments (clear)

  1. Overkill by Tubal-Cain · · Score: 5, Funny

    You should only need 42.

  2. reductionism by Anonymous Coward · · Score: 2, Insightful

    Highly speculative and reductionistic. Just because you can reduce things down to a lower level of complexity, it doesn't mean that this reduced set of molecules explain everything life related.

    Well I guess it's a step up from the widespread public perception that DNA determines everything.

    1. Re:reductionism by philspear · · Score: 3, Funny

      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.

  3. So..... by RollinDutchMasters · · Score: 3, Insightful

    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.

    1. Re:So..... by gnick · · Score: 3, Informative

      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.

      --
      He's getting rather old, but he's a good mouse.
  4. Are 2 Bits Enough To Understand Computers? by Anonymous Coward · · Score: 5, Funny

    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.

    1. Re:Are 2 Bits Enough To Understand Computers? by Ethanol-fueled · · Score: 4, Funny

      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.

  5. Only 68? Piece of cake! by A+nonymous+Coward · · Score: 2, Insightful

    Of course, two of those 68 molecules are RNA and DNA. The other 66 should be cake for anyone who understands either one of them.

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    Infuriate left and right
  6. Re:How many were you expecting? by jellomizer · · Score: 4, Insightful

    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.

    --
    If something is so important that you feel the need to post it on the internet... It probably isn't that important.
  7. Obvious and boring by Cougem · · Score: 5, Insightful

    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.

    1. Re:Obvious and boring by OG · · Score: 5, Insightful

      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.

    2. Re:Obvious and boring by OG · · Score: 4, Informative

      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.

    3. Re:Obvious and boring by RollinDutchMasters · · Score: 2, Informative

      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.

      I had a table with that molecular breakdown in my biochem textbook. It was just black&white instead of colored, and it didn't look like it was made in Illustrator.

      Way to go to him for... coloring... I guess. It's still pretty 1970-y information.

    4. Re:Obvious and boring by Anonymous Coward · · Score: 3, Funny

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

      * Applause *

    5. Re:Obvious and boring by philspear · · Score: 4, Insightful

      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.

    6. Re:Obvious and boring by Goldsmith · · Score: 2, Interesting

      I completely agree with Marth's conclusion, but his letter is not insightful, he's simply registering a complaint about the rise of proteomics. It's not a research article, it's a letter to the editor. We get the same things in physics journals lamenting the rise of string theory or the decrease in funding for superconductivity.

      Marth's call for interdisciplinary research and fresh ideas is good, but he's already made a mistake by grouping the molecules together using his own judgment. It would be better to present them all to a widely varying group of scientists and ask them to group the molecules in any way they would like. The idea that there are ~100 important biological building blocks is not new. But... this is just a letter to the editor, and the poster looks good, and we get the idea. Roland should not have picked it up, and it shouldn't be here, it was probably written for a department head somewhere who doesn't want to fund a new interdisciplinary program.

    7. Re:Obvious and boring by Anonymous Coward · · Score: 3, Insightful

      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.

    8. Re:Obvious and boring by Compuser · · Score: 2, Interesting

      For someone who supposedly did a lot of surveying of the field he somehow missed an important amino acid: citrulline which is very important because many proteins undergo deimination and it results in change of function. And this is just from what I caught right off the bat. Let's just say I do not think the world of this article and the "quite a bit of information" is really "way too simplistic view".

    9. Re:Obvious and boring by Hasmanean · · Score: 2, Interesting

      >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?

      The ancient Greeks and alchemists too, thought the soul was a chemical, and even today the modern pharmaceutical industry seems to think medicine should be about finding chemicals to magically give us health. Biologists are a lower form of life than hackers, they're drip-kiddies.

      It's like an analog hardware engineer I knew who didn't appreciate the complexity of software, and would say (half-jokingly) "it's all an analog voltage when you get down to it." The funny thing is, when I helped him with his software problems, the longer he tried to describe the code to me, the less I understood of it. He had a hardware engineer's mind: to him the whole program was something to be analyzed simultaneously, not as a step-by-step sequential modification of the data. I think he would have loved programming in prolog.

      --
      Hasan
  8. Re:Obligatory. by krgallagher · · Score: 4, Funny
    "68 should be enough for anyone."

    When he tried for 69, he blew it.

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    Insert Generic Sig Here:

  9. Re:woo by pesho · · Score: 5, Funny

    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.

  10. Who submitted it? (was: Re:Obvious and boring) by siglercm · · Score: 5, Insightful

    How did this make slashdot?

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

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    sigfault (core dumped)
    1. Re:Who submitted it? (was: Re:Obvious and boring) by Anonymous Coward · · Score: 2, Interesting

      the really interesting thing is that roland never gets *any* rejects, no matter how shitty his submissions.

    2. Re:Who submitted it? (was: Re:Obvious and boring) by Hal_Porter · · Score: 2, Funny

      Ever since he submitted that story about mind control and manipulation.

      --
      echo -e 'global _start\n _start:\n mov eax, 2\n int 80h\n jmp _start' > a.asm; nasm a.asm -f elf; ld a.o -o a;
  11. Re:How many were you expecting? by Kingrames · · Score: 4, Funny

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

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    If you can read this, I forgot to post anonymously.
  12. Mendeleev! by TrashGod · · Score: 2, Informative

    From TFA: "Like the periodic table of elements, first published in 1869 by Russian chemist Dmitri Mendeleev, is to chemistry, Marth's visual metaphor offers a new framework for biologists." OK, the article is thin and the work derivative, but the picture shows promise. I like any decent web-based periodic table, it just need links.

  13. Re:How many were you expecting? by gnick · · Score: 3, Funny

    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

    --
    He's getting rather old, but he's a good mouse.
  14. Re:woo by LiquidHAL · · Score: 3, Funny

    Strings. Science over.

  15. Some Context by OG · · Score: 4, Informative

    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.

    1. Re:Some Context by lgw · · Score: 2, Interesting

      Ifit had been properly summarized, it would have been fine. "The Cell: Not Just Software."

      --
      Socialism: a lie told by totalitarians and believed by fools.
  16. Improved Summary by SlashDotDotDot · · Score: 3, Insightful

    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.

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    /...
  17. this guy does something with sugars? by nietsch · · Score: 2, Interesting

    34 separate (common) sugars, + sugar-protein, sugar lipid combinations. Something tells me this guy has some stake in the acceptance of sugars in cell biology. By including the buildingblocks of DNA and RNA, but not their sequences and regulating factors, he skews the board drastically for his cause. Maybe he is right and there are some diseases dependent on attached sugar groups. But thus far, these are swamped by the number of confirmed diseases caused by mutations in the DNA, or infections by viruses, bacteria or protozoa.

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    This space is intentionally staring blankly at you
  18. Probably right, probably useless by gmuslera · · Score: 2, Insightful

    26 letters are enough to understand all english (and most of the other languages) literature?

    Wonder what must be using the infinite amount of monkeys instead of typewriters to generate all possible mixes of those 68 molecules.

  19. In other misrepresentations... by Arthur+Grumbine · · Score: 5, Funny

    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?

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    Now that I think about it, I'm pretty sure everything I just said is completely wrong.
  20. Obligatory by Anonymous Coward · · Score: 2, Funny

    68 molecules ought to be enough for everyone!!

  21. Re:How many were you expecting? by gnick · · Score: 3, Funny

    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.

    --
    He's getting rather old, but he's a good mouse.
  22. Re:Electrons, Protons and Neutrons! by Arcturax · · Score: 2, Insightful

    Because Roland posted it. Seriously.

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    --Won't that be grand? Computers and the programs will start thinking and the people will stop. - Dr. Walter Gibbs
  23. Sounds familiar... by markhb · · Score: 2, Insightful

    This sounds a lot like the idea that you can derive all of electromagnetic physics from Maxwell's equations. It may be true, but don't try to do it during the test.

    --
    Save Maine's economy: write stuff down. All comments are exclusively my own, not my employer.
  24. Re:I've got 2 bits... by bob_herrick · · Score: 4, Funny

    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!

  25. Water by mosb1000 · · Score: 3, Insightful

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