Comments on: Public Library of Science http://www.arsmathematica.net/2007/02/14/public-library-of-science/ Dedicated to the mathematical arts. Fri, 29 May 2015 09:17:44 +0000 hourly 1 https://wordpress.org/?v=4.1.41 By: Chris Leonard http://www.arsmathematica.net/2007/02/14/public-library-of-science/#comment-6103 Fri, 16 Feb 2007 09:55:17 +0000 http://www.arsmathematica.net/archives/2007/02/14/public-library-of-science/#comment-6103 In repsonse to Walt’s request for more info on the forthcoming PhysMath Central, please see this recent interview we did with First Author.

Regards,
Chris

http://www.firstauthor.org/Downloads/BMC.pdf

]]> By: Chris Grant http://www.arsmathematica.net/2007/02/14/public-library-of-science/#comment-5982 Thu, 15 Feb 2007 22:53:24 +0000 http://www.arsmathematica.net/archives/2007/02/14/public-library-of-science/#comment-5982 Kenny:

Have you had any thoughts of broadening your business model beyond the academic community? Maybe start an online retailer (Nozama.com?) in which readers for books can be purchased instead of vice versa? That would be something.

]]> By: Kenny Easwaran http://www.arsmathematica.net/2007/02/14/public-library-of-science/#comment-5961 Thu, 15 Feb 2007 20:45:14 +0000 http://www.arsmathematica.net/archives/2007/02/14/public-library-of-science/#comment-5961 Chris Grant – the entire point of this exercise is that these publications are of positive value to readers, but the readers have drastically different values for money (depending on whether they’re graduate students or tenured professors, and in the US or a developing country) so a price-based distribution system makes it available to people in a way that doesn’t have all that much correlation to the value it has for people. But just as the publication has positive value, so does the readership. So it also makes sense to charge the author, since she wants as many people as possible to know about her work. If we required a monetary transaction every time someone gained value, then since publishing is a radically non-zero-sum game, we’d just be pouring money into a hole somewhere.

]]> By: Jonathan Vos Post http://www.arsmathematica.net/2007/02/14/public-library-of-science/#comment-5937 Thu, 15 Feb 2007 18:57:05 +0000 http://www.arsmathematica.net/archives/2007/02/14/public-library-of-science/#comment-5937 One purpose of Open Access science is that one can do postmodernist “mashups” of the data in them, for purposes akin to mowing lawns for tenure.

For example:

Dark Bands in the Human Spectrum
by
Jonathan Vos Post
Computer Futures, Inc.
jvospost2@yahoo.com
draft 2.0 of 2 Feb 2007, 27 pp., expands 1.0 of 1 Feb 2007

What is the human body made of? An odd way to answer this is with the inverse question: What is the human body NOT made of? I can give an answer in the following sense: for what natural numbers (i.e. positive integers) is there no ion or molecule found
in significant quantities in a human being, which has that number as the average atomic or molecular weight, rounded down?

Humans have lots of water, and thus lots of hydrogen atoms and hydrogen ions, both of whose molecular weights (1.00783) round down to the integer 1. Heavy water (deuterium oxide) has already been figured in by our using an average molecular weight, which this considers both protium (hydrogen with no neutron) and deuterium (hydrogen with a neutron, molecular weight averaged down to 2). There is not going to be a measurable amount of radioactive tritium (hydrogen with two neutrons) whose atomic weight rounds down to 3.

The human body has essentially no helium (atomic weight rounded down to 3 for the rare light isotope, rounded down to 4 for the common isotope). The human body, assuming this is not a person taking lithium as treatment for depression, has nothing of molecular weight 5, 6, or 7. Beryllium is rare, and a poison. So there is a gap in the average molecular weight mass spectrum of a human which is covered by the integers 2 through 10. There should be no atomic carbon in a human body, not counting gunshot residue or charcoal from grilling or sketching, hence no 12 or 13. Carbon is in humans, but bound up in organic molecules.

In summary, the integers representing mass gaps in the human spectrum include:
2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 19, 20, 21, 24, 25, 36, 37, 40, 41, 42, 49, 52, 53, 56, 64, 66, 69, 70, 82, 91, 95, 98, 99, 107.

We’ll look higher, but these “dark bands” will become rare. There are no more such dark bands through 150…

Source of data: the Human Metabolome Data Base

We may also take this as the human biochemistry analogue to the [OEIS] Online Encyclopedia of Integer Sequences entry whose database is the periodic table,
“A070217 Numbers not represented by a known atomic weight.”

On 1/31/07, Jonathan Post wrote:
Sorted (by hand) by molecular weight

HMDB02106 1.00783 Hydrogen ion
HMDB01362 1.00783 Hydrogen
HMDB02386 11.00930 Boron
HMDB02714 16.03130 Methane
HMDB01039 17.00274 Hydroxide
HMDB00051 17.02655 Ammonia
HMDB02111 18.01060 Water
HMDB00662 18.99840 Fluorine
HMDB00588 22.98980 Sodium
HMDB00547 23.98504 Magnesium
HMDB02084 26.00307 Cyanide
HMDB02175 27.97690 Silicon
HMDB01361 27.99490 Carbon
HMDB01371 28.00610 Nitrogen
HMDB03378 29.99799 Nitric oxide
HMDB01426 30.01056 Formaldehyde
HMDB01315 30.97380 Phosphorus
HMDB00164 31.04220 Methylamine
HMDB02983 31.04220 Methylamine Hydrochloride
HMDB00598 31.97210 Sulfur
HMDB01377 31.98980 Oxygen
HMDB02168 31.98983 Superoxide
HMDB01875 32.02621 Methanol
HMDB03338 33.02150 Hydroxylamine
HMDB00983 33.98770 Hydrogen Sulfide
HMDB00492 34.96885 Chlorine
HMDB02162 35.97670 Hydrochloric acid
HMDB02306 35.97670 Hydrochloric acid
HMDB00586 38.96371 Potassium
HMDB00464 39.96260 Calcium
HMDB02078 43.00580 Cyanate
HMDB01967 43.98980 Carbon Dioxide
HMDB00990 44.02621 Acetaldehyde
HMDB01536 45.02146 Formamide
HMDB00087 45.05785 Dimethylamine
HMDB00142 46.00548 Formic acid
HMDB00108 46.04186 Ethanol
HMDB01382 47.00070 Nitrite
HMDB03227 48.00337 Methanethiol
HMDB02503 50.94400 Vanadium
HMDB01050 50.96377 Hypochlorite
HMDB00599 51.94050 Chromium
HMDB01333 54.93800 Manganese
HMDB00692 55.93490 Iron
HMDB02457 57.93530 Nickel
HMDB01659 58.04186 Acetone
HMDB03366 58.04190 Propanal
HMDB00608 58.93320 Cobalt
HMDB01842 59.04835 Guanidine
HMDB01869 59.03710 Acetamide
HMDB03656 59.03710 Acetaldehyde oxime
HMDB00906 59.07350 Trimethylamine
HMDB03551 60.00855 Carbamate
HMDB03344 60.02110 Glycolaldehyde
HMDB00042 60.02113 Acetic acid
HMDB00294 60.03236 Urea
HMDB00820 60.05751 Propyl alcohol
HMDB00863 60.05751 Isopropyl alcohol
HMDB00595 60.99257 Hydrogen Carbonate
HMDB00149 61.05276 Ethanolamine
HMDB02179 61.98782 Peroxynitrite
HMDB02878 61.98782 Nitrate
HMDB03538 62.00040 Carbonic acid
HMDB02303 62.01902 Dimethylsulfide
HMDB01887 62.03678 Ethylene glycol
HMDB00657 62.92960 Copper
HMDB01853 62.99560 Nitrate
HMDB01303 63.92910 Zinc
HMDB03276 65.95979 Hydrogen sulfide
HMDB02077 67.96650 Chlorite
HMDB01525 68.03745 Imidazole
HMDB04101 71.06092 beta-Aminopropionitrile
HMDB01167 72.02113 Pyruvaldehyde
HMDB03543 72.05750 Butanal
HMDB00474 72.05751 Butanone
HMDB01106 73.05276 3-Aminopropionaldehyde
HMDB02134 73.05276 Aminoacetone
HMDB01522 73.06400 Methylguanidine
HMDB02501 73.92120 Germanium
HMDB00119 74.00039 Glyoxylic acid
HMDB00237 74.03678 Propionic acid
HMDB03052 74.03678 Lactaldehyde
HMDB03453 74.03680 3-Hydroxypropanal
HMDB04327 74.07320 1-Butanol
HMDB00002 74.08440 1,3-Diaminopropane
HMDB00123 75.03203 Glycine
HMDB00925 75.06841 Trimethylamine oxide
HMDB00115 76.01604 Glycolic acid
HMDB01881 76.05243 1,2-Propanediol
HMDB02808 76.05243 1,3-Propanediol
HMDB02991 77.02992 Cysteamine
HMDB02151 78.01390 Dimethyl sulfoxide
HMDB01505 78.04695 Benzene
HMDB02500 78.91834 Bromine
HMDB00926 79.04220 Pyridine
HMDB01349 79.91652 Selenium
HMDB00240 79.95681 Sulfite
HMDB01033 80.96464 Hydrogen Sulfite
HMDB03008 81.97246 Bisulfite
HMDB03929 83.04830 5-Aminoimidazole
HMDB02036 83.96140 Chloric acid
HMDB04363 84.03240 Imidazolone
HMDB02039 85.05276 2-Pyrrolidinone
HMDB00549 86.03678 4-Deoxytetronic acid
HMDB02523 86.03678 Oxolan-3-one
HMDB03407 86.03680 Diacetyl
HMDB01080 87.06841 4-Aminobutyraldehyde
HMDB03642 87.90560 Strontium
HMDB01880 87.97966 Hydrogen Oxalate
HMDB00243 88.01604 Pyruvic acid
HMDB00039 88.05243 Butyric acid
HMDB01873 88.05243 Isobutyric acid
HMDB03243 88.05243 Acetoin
HMDB01414 88.10005 Putrescine
HMDB02435 89.01129 (hydroxyimino)-Acetic acid
HMDB00056 89.04768 b-Alanine
HMDB00161 89.04768 L-Alanine
HMDB00271 89.04768 Sarcosine
HMDB02329 89.99531 Oxalic acid
HMDB00190 90.03169 L-Lactic acid
HMDB00700 90.03169 Hydroxypropionic acid
HMDB01051 90.03169 Glyceraldehyde
HMDB01311 90.03169 D-Lactic acid
HMDB01882 90.03169 Dihydroxyacetone
HMDB03156 90.06808 2,3-Butanediol
HMDB03692 90.06810 (S,S)-Butane-2,3-diol
HMDB00131 92.04734 Glycerol
HMDB03012 93.05785 Aniline
HMDB04983 94.00890 Dimethyl sulfone
HMDB00228 94.04186 Phenol
HMDB01429 94.95510 Phosphate
HMDB00979 96.95955 Hydrogen Sulfate
HMDB00973 96.96907 Hydrogen phosphate
HMDB02105 96.96907 Dihydrogen Phosphate
HMDB01302 97.90540 Molybdenum
HMDB02934 97.96738 Sulfuric acid
HMDB01448 97.96740 Sulfate

[truncated here, but you get my drift…]

]]> By: Peter http://www.arsmathematica.net/2007/02/14/public-library-of-science/#comment-5932 Thu, 15 Feb 2007 18:03:37 +0000 http://www.arsmathematica.net/archives/2007/02/14/public-library-of-science/#comment-5932 Of course, it will rarely be the actual authors themselves you will pay for publication. Most academic authors will use their research grants to pay these fees, so it will be the long-suffering, general public whose taxes pay for research grants, who will ultimately pay the fees. This does seem grossly unfair. If the research is actually of value to somebody, then that somebody should pay for publication, not the general public. If the research upon which the publications are based is paid-for by research grants arising from public taxation, then surely the results should be published in the free-to-read and free-to-write public domain.

]]> By: Chris Grant http://www.arsmathematica.net/2007/02/14/public-library-of-science/#comment-5931 Thu, 15 Feb 2007 18:01:21 +0000 http://www.arsmathematica.net/archives/2007/02/14/public-library-of-science/#comment-5931 Walt writes: “If neighborhood kids could get tenure by mowing your lawn, they’d be out there right now, gratis.”

You must live in a different sort of neighborhood than I do. And that you can force someone to do absurd things by holding a threat like denial of tenure over their heads doesn’t make the practice any less absurd. If academics are truly producing something of value, why can’t the market recognize that instead of fining them for being productive? I don’t and won’t pay page charges, and I spend a lot of my own money buying access to work that others have produced. To me that makes a lot more sense than the alternative, but YMMV.

]]> By: Walt http://www.arsmathematica.net/2007/02/14/public-library-of-science/#comment-5924 Thu, 15 Feb 2007 17:23:05 +0000 http://www.arsmathematica.net/archives/2007/02/14/public-library-of-science/#comment-5924 Chris Leonard: This is the first I’ve heard about PhysMathCentral, and there’s not much detail on your website. What do you have planned?

]]> By: Walt http://www.arsmathematica.net/2007/02/14/public-library-of-science/#comment-5923 Thu, 15 Feb 2007 17:21:19 +0000 http://www.arsmathematica.net/archives/2007/02/14/public-library-of-science/#comment-5923 The difference between vanity presses and academic presses is small indeed. (Academia is at least a kind of collective vanity.) Author fees are common in fields with a lot of grant money. The reason being is that the certification process of appearing in a prestigious journal is of positive value to the author as well as the readers. If neighborhood kids could get tenure by mowing your lawn, they’d be out there right now, gratis.

]]> By: Chris Grant http://www.arsmathematica.net/2007/02/14/public-library-of-science/#comment-5914 Thu, 15 Feb 2007 16:25:55 +0000 http://www.arsmathematica.net/archives/2007/02/14/public-library-of-science/#comment-5914 So if these articles are of positive value, why make the producers of these articles pay rather than the consumers? Maybe I’ll start charging the neighborhood kids for the privilege of mowing my lawn.

]]> By: Chris Leonard http://www.arsmathematica.net/2007/02/14/public-library-of-science/#comment-5913 Thu, 15 Feb 2007 16:15:37 +0000 http://www.arsmathematica.net/archives/2007/02/14/public-library-of-science/#comment-5913 >> Are these publications of positive value or not?

Well, that is up to the scientific community to decide. Both PLoS and BioMed Central have stringent peer-review stages to pass before acceptance and both seem to have higher than average impact factors, so the answer would seem to be ‘yes’.

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