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Are 68 Molecules Enough To Understand Diseases? 133

Posted by ScuttleMonkey
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.'"
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Are 68 Molecules Enough To Understand Diseases?

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  • Overkill (Score:5, Funny)

    by Tubal-Cain (1289912) on Monday September 08, 2008 @03:38PM (#24923955) Journal

    You should only need 42.

  • Doesn't seem like that low a number. What's the big deal?

  • reductionism (Score:2, Insightful)

    by Anonymous Coward

    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.

    • by philspear (1142299) on Monday September 08, 2008 @04:17PM (#24924475)

      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.

    • by Stooshie (993666)

      Yeh, cause the periodic table wasn't useful. We shoulda just scrapped that reductionistic nonsense.

      Of course reducing things to a lower level, in itself, doesn't help, but the great thing here is being able to look at molecular biology in a different way. (OK, it may have been implicitly known, but no-one explicitly stated it so clearly).

      It is now explicitly stated that there are only 68 molecules that play any major part in life. That's a massive step forward.

      Scientists can now concentrate on these

      • by galoise (977950)

        until we find a bacteria that has a 69th molecule in its chemical composition, and then its all over again.

        Actually, by having a delimited taxonomy we might overlook some critical aspect related to this hypothetical 69th molecule, etc etc.

        This is a classic problem in epistemology. Taxonomies are of no worth if they do not produce a cognitive change unavailable without the formulation of the taxonomy. Limiting the number of elements in a set is not in itself a great leap forward for science, unless you can e

  • Obligatory. (Score:1, Redundant)

    68 should be enough for anyone.

  • So..... (Score:3, Insightful)

    by RollinDutchMasters (932329) on Monday September 08, 2008 @03:40PM (#24923985)
    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.
  • by Anonymous Coward on Monday September 08, 2008 @03:41PM (#24923993)

    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.

  • by A nonymous Coward (7548) * on Monday September 08, 2008 @03:44PM (#24924023)

    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.

    • by Gat0r30y (957941)
      there are 8 nucleosides. They are part of the 68 count, so really 60.
    • by unfasten (1335957)
      Actually he's saying that the 68 molecules are used to build those components, not that they're part of the 68 molecules:

      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,'

  • I got 68 molecules but a glycan ain't one of 'em.

  • Even better, all you need to understand why your computer doesn't boot is the 37 fundamental building blocks of computers, roughly divided into the plastics (acrylic, etc.), liquid crystals, metals (steel, iron, copper, silver, etc.), and silicon.

    Now, go fix that BSOD.

    • by g-san (93038)

      well it might blow you away to find out that everything your cpu does is load, store, add, subtract, branch and some bitwise operators.

  • Obvious and boring (Score:5, Insightful)

    by Cougem (734635) on Monday September 08, 2008 @03:48PM (#24924103)
    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.
    • by siglercm (6059) on Monday September 08, 2008 @04:01PM (#24924255) Journal

      How did this make slashdot?

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

      • by zullnero (833754)
        Hey, at least he's not linking through his blog anymore.
        • by Arcturax (454188)

          His blog is still just a regurgitation of the articles and at times outright ripped straight from it.

          This guy is a blog spammer. He is still using /. to get more hits to his blog and to get himself a higher ranking in google. He also gets posted more often than is fair to other users. It's obvious at this point he is getting special treatment from /.

          Between this and all the other controversies in the past (Michael, mass mod bitch slaps, etc), I am starting to reconsider continuing to contribute anything

          • Re: (Score:2, Interesting)

            by Anonymous Coward

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

    • by OG (15008) on Monday September 08, 2008 @04:03PM (#24924293)

      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: (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.

      • by philspear (1142299) on Monday September 08, 2008 @04:35PM (#24924789)

        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.

        • 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.

          Sounds like a job for http://innocentive.com [www.http] .

        • You mentioned lipid rafts, and to drive the point home, I would cite a type of lipid called inositol phosphates. These lipids have 5 positions available for modification by phosphorylation. And there are 7 possible lipids that are commonly found in the cell (http://dx.doi.org/10.1016/j.tibs.2008.07.002). Separating these things apart is a nightmare ...
      • Re: (Score:3, Interesting)

        by Goldsmith (561202)

        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

      • Re: (Score:3, Insightful)

        by 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: (Score:3, Interesting)

        by Compuser (14899)

        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".

    • I agree with the gist of your post (though not necessarily the tone)... but

      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

    • 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.

      Except it's not a simple organic molecule, but an inorganic mineral. Organic != Biogenic.

    • by l0ungeb0y (442022)

      "What about hydroxyapatite?"

      You know, now that you mention it, I have an appetite for Hydrox as well. Haven't seen them around in years though. Shame.

    • Bzzzt! Point three is wrong.

      To quote the paper in Nature:

      "Unlike the genome and proteome, the glycome and lipidome are not directly encoded by DNA. Nevertheless, the glycome and the lipidome contribute to the pathogenesis and severity of an increasing number of diseases,..."

      The whole point of the author's paper is that we need to understand more than the molecules which make generic material if we are to understand disease. The significance of the number 68 is that it is greater than the number of molecul

    • Re: (Score:2, Interesting)

      by Hasmanean (814562)

      >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 softw

  • by nomadic (141991)
    And I correctly determined that 100% of diseases are caused by some combination of only 117 atomic elements. Give me my Nobel.
    • Re:woo (Score:5, Funny)

      by pesho (843750) on Monday September 08, 2008 @04:00PM (#24924239)
      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.
      • by Eudial (590661)

        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.

        It's icky to compare electrons to protons and neutrons. You really need to break it all down into fermions.

        What you'll end up with is Up-quarks, down-quarks and electrons (possibly positrons).

        Furthermore, to bind these together, you'll want strong, weak and electromagnetic forces. So, add to that W bosons, Z bosons and photons. Gravity is a non-issue on a subatomic level, so we don't need gravitons. Perhaps Higgs bosons if they do exist.

        But still, that's a lot fewer than 117.

      • Re: (Score:3, Funny)

        by LiquidHAL (801263)
        Strings. Science over.
        • I understand your point. Once you have three particles, you are computationally screwed. So anything bigger than hydrogen is a bummer. Best to avoid particles altogether. String theory starts from the philosophical position that the universe is pointless, but vibrators make it endurable. I'm told it is a wonderland of elegant maths. Well, about 10^500 wonder-universes apparently. However, I object to strings being so pushy. What about the rest of the orchestra. Percussion got their star turn at the big ban
    • That's an ironic sort of comment. I'll bet you didn't RTFA:

      Reviewing findings from multiple disciplines, Jamey Marth, Ph.D... 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...

      Like the periodic table of elements ... is to chemistry, Marth's visual metaphor offers a new framework for biologists.

    • by g-san (93038)

      So you imply that watching one child play with a ball would give you an understanding of international politics? You would have to be pretty blind to not see that there are several levels there, and it helps to define and delineate those levels to help understand the whole thing.

  • This might not be obvious to some : the study is saying that there are 68 *types* of molecules to build up cells.

    The fact that they propose a closed number -- not necessarily that it's a small or large number -- is interesting. However, I wouldn't be surprised if this number increased, as our knowledge of the biochemistry of archaea, viruses and other organisms increases. It's like saying the current status of the periodic table of known elements is finished.
  • Mendeleev! (Score:2, Informative)

    by TrashGod (752833)
    From TFA: "Like the periodic table of elements, first published in 1869 by Russian chemist Dmitri Mendeleev [wikipedia.org], 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 [ucsd.edu] shows promise. I like any decent web-based periodic table, it just need links.
  • I've got 2 bits, a 0 and 1, I can encode almost any piece of information in it. Even a 2 year old can understand 0 and 1!!!

    This stuff is easy.

  • I can go even further and break it all down to 1s and 0s.

    Noble Prize for Medical Breakthrough here I come!
  • ... have been found necessary to replicate all known English language poetry, prose, social and political literature, and scientific and technical writings. This includes such works foundational to the development of the post-modern age as Newton's Principia, Shakespeare's plays and sonnets, Feynman's lectures, Friedman's works on economics, and so forth.

    Big whoop.

    • by maxume (22995)

      Whoops

        have been found necessary to replicate all known English language poetry prose social and political literature and scientific and technical writings This includes such works foundational to the development of the postmodern age as Newtons Principia Shakespeares plays and sonnets Feynmans lectures Friedmans works on economics and so forth

      Big whoop

    • by mikiN (75494)

      i want my capital letters comma period exclamation mark question mark apostrophe opening and closing quotes and parentheses em and en dash underscore etc
      or do you want me to write all of those in longhand
      never mind

  • I've managed to reduce all 68 of these molecules to a single commonality: Carbon!

    Curing diseases with this information is left as an exercise for the reader. Just send me the Nobel Prize. Thanks. Couldn't have done it without Slashdot.

  • ...a distinguished chemist has announced that by his calculations less than 100 elements are required to explain the material composition of all of the earth's problems How simple it all seems, suddenly. :)

  • Some Context (Score:5, Informative)

    by OG (15008) on Monday September 08, 2008 @04:36PM (#24924803)

    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.

    • Re: (Score:3, Interesting)

      by lgw (121541)

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

    • by tfoss (203340)

      I generally agree with your post, but will pick one nit:

      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.

      Many non-biology scientists may have thought that, people who actually work in the field were far less naive about it. Knowing the genome provides a *lot* of information, but is far from complete.

      A well-known scientist I talked to made the pretty interesting analogy of a cell to a large city. Decoding the genome is like obtaining a phone book for the city...but only the white pages. You know everyone who lives there, but you don't have any idea wh

  • Improved Summary (Score:3, Insightful)

    by SlashDotDotDot (1356809) on Monday September 08, 2008 @04:40PM (#24924881) Journal

    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 [primidi.com] and Thomas Joseph [blogspot.com] offer commentary on their blogs.

  • by nietsch (112711) on Monday September 08, 2008 @04:42PM (#24924915) Homepage Journal

    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.

    • Re: (Score:1, Interesting)

      by Anonymous Coward

      Definitely - he's a glycobiologist. The glycobiologists have been making their case for acceptance for a long time now.

      This is pretty much standard stuff (especially with the quote from Varki) from the glyco crowd.

      I actually don't think the glyco world is that complex (at least in the mammalian systems - bacterial glycans are significantly more complex). I also don't know what their hidden agenda is, maybe it's coming up to time to get some projects funded, and they want to convince the NIH that they are ac

    • by g-san (93038)

      "these are swamped by the number of confirmed diseases caused by mutations in the DNA..."

      Right. Normally a mutation is dealt with. DNA can repair itself, something will break down incorrectly built proteins, bad DNA making bad cell parts will kill themselves. Understanding why this doesn't always work is worthwhile.

      "...or infections by viruses, bacteria or protozoa."

      It's my understanding that a virus has to penetrate the cell well to infect a cell. See all that hair on the cell wall in blue in the diagram?

  • by gmuslera (3436) on Monday September 08, 2008 @04:42PM (#24924931) Homepage Journal
    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.
  • It seems all cellular function is a result of interactions between protons, neutrons, and electrons in assorted arrangements.
  • Sounds familiar... (Score:3, Insightful)

    by markhb (11721) on Monday September 08, 2008 @05:23PM (#24925527) Journal

    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.

  • For computer viruses, you only need to understand 1's and 0's.

  • Water (Score:4, Insightful)

    by mosb1000 (710161) <mosb1000@mac.com> on Monday September 08, 2008 @06:35PM (#24926433)

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

  • And the human body is just eighty-nine cents worth of chemicals.

    And you can explain everything with just ninety-two elements. Or just four, earth, air, water, and fire.

    One of the most amazingly mind-opening things I ever read was a remark in a book by John R. Pierce, to the effect that Kirchoff's Laws are more general than Maxwell's Equations, because they can explain the behavior of all circuits, not just electronic circuits... but that Maxwell's Equations are more general than Kirchoff's Laws because they

  • only 68 molecular building blocks are used to construct these four fundamental components of cells

    In other news, Microsoft is only interested in controlling two areas of digital computing: the zeros and the ones.

  • which tells you nothing of the content or the meaning.
  • That's how this game works right?

  • What about porphyrins?
    photosynthesis, oxygen transport, electron transfer, and so on.
    I guess this is a case of "your favorite molecule sucks."
  • we can explain the economy by looking at one, five, ten, etc dollar bills.

He keeps differentiating, flying off on a tangent.

Working...