[Taxacom] Phylogenetic Game
Simon Mayo
simonjosephmayo at hotmail.co.uk
Fri Dec 10 12:12:39 CST 2010
Dear Peter,
Idealistic morphology rears its head again in a new guise! Phylogeny is only interpretation of patterns ....
Simon Mayo
> From: taxacom-request at mailman.nhm.ku.edu
> Subject: Taxacom Digest, Vol 57, Issue 9
> To: taxacom at mailman.nhm.ku.edu
> Date: Fri, 10 Dec 2010 12:00:01 -0600
>
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> Today's Topics:
>
> 1. protection of specimens (Vlastimil Mikolas)
> 2. Re: protection of specimens (Hans Henderickx)
> 3. Checklist of World Grasses (Simon Bryan)
> 4. Phylogenetic Game (Peter Stevens)
> 5. Re: Phylogenetic Game (John Grehan)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 9 Dec 2010 20:26:10 +0100
> From: Vlastimil Mikolas <dolomiticola at gmail.com>
> Subject: [Taxacom] protection of specimens
> To: taxacom at mailman.nhm.ku.edu
> Message-ID:
> <AANLkTi=vjwtyGpoFeFGjWxmknbzbe_hFoWNu9ByaLZHQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Taxacomers,
> I have many herb. specimens from Slovakia and adjacent Europe, including
> many tax. critical taxa (all determined), however I have not enough of money
> fo payment of rents of rooms with specimens. If you have interest in
> specimens and can slightly to help me, write me. Many thanks !
> Cordial best,
> Vlastimil
>
> --
> Vlastimil MIKOLAS
> Hanojska 4
> SK-040 13 KOSICE
> Slovakia
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 9 Dec 2010 20:56:58 +0100
> From: "Hans Henderickx" <cavexplorer at gmail.com>
> Subject: Re: [Taxacom] protection of specimens
> To: "Vlastimil Mikolas" <dolomiticola at gmail.com>,
> <taxacom at mailman.nhm.ku.edu>
> Message-ID: <4F8B815CC2AB491C975F77C0DF7D47F5 at cavex76040a5ab>
> Content-Type: text/plain; format=flowed; charset="iso-8859-1";
> reply-type=original
>
> That is interesting, Vlastimil. Than why did you collect them?
> Hans
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 10 Dec 2010 13:13:22 +1000
> From: "Simon Bryan" <bryan.simon at derm.qld.gov.au>
> Subject: [Taxacom] Checklist of World Grasses
> To: <taxacom at mailman.nhm.ku.edu>
> Message-ID:
> <FA14B37EFE33F647B409C8B24F40D169019CDA18 at MINMAIL4.lands.resnet.qg>
> Content-Type: text/plain; charset="us-ascii"
>
> A check-list of currently accepted species of grasses of the world can
> be found at the GrassWorld Scratchpad
> http://grassworld.myspecies.info/content/check-list-world-grasses
> The first list includes authors, place of publication and TDWG Level 1
> distributions (Europe, Africa, Temperate Asia, Tropical Asia,
> Australasia, Pacific, North America, South America, Antarctic.) and
> classification, where subfamilies, tribes and genera follow GPWG and
> subsequent grass taxonomic literature.
> Lists of each Continental Region follow, with TDWG Level 3 distributions
> indicated. Distributional information has been gleaned from the
> agrostological literature, the Kew SYNON access database and TROPICOS.
> Feedback from users would be much appreciated in cases where information
> is noted to be incorrect or where different distributional information
> from that given in this check-list is known. Exchange of such
> information can be placed in the Forums section of the GrassWorld
> Scratchpad.
> It is possible to provide a list of grasses to interested parties of any
> country of the world or region of larger countries (Russia, China,
> India, USA, Canada, Brazil, Argentina, Chile, Mexico, Australia, South
> Africa) where this information is available.
> Bryan Simon
> Principal Botanist
> Queensland Herbarium
> DERM, Brisbane Botanic Gardens
> Mt Coot-tha, Toowong, Qld 4066
> Australia
>
>
>
>
> +----------------------------------------------------------------+
> Think B4U Print
> 1 ream of paper = 6% of a tree and 5.4kg CO2 in the atmosphere
> 3 sheets of A4 paper = 1 litre of water
> +----------------------------------------------------------------+
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 10 Dec 2010 11:02:09 -0600
> From: Peter Stevens <peter.stevens at mobot.org>
> Subject: [Taxacom] Phylogenetic Game
> To: TAXACOM <taxacom at mailman.nhm.ku.edu>
> Message-ID: <C8CF6F50-1BB9-4DBD-836D-8A0FB85468D7 at mobot.org>
> Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes;
> format=flowed
>
> Note that "Players don't need to understand (or even care about)
> phylogenetics."
>
> P.
>
> Subject: Phylogenetics game
>
> December 2, 2010 | A pattern-matching puzzle created by
> bioinformaticians at McGill University lets players sort genetic
> code. The game, called Phylo, takes advantage of the human brain's
> efficiency at recognizing and sorting patterns to tackle multiple
> sequence alignments.
>
> Aligning genetic sequences is traditionally done computationally, but
> what is a huge computational problem, is a bit easier for the human
> brain. ?There are some calculations that the human brain does more
> efficiently than any computer can, such as recognizing a face,?
> explained lead researcher J?r?me Waldispuhl of the School of Computer
> Science in a McGill press release. ?Recognizing and sorting the
> patterns in the human genetic code falls in that category."
>
> Players don't start from scratch, but instead refine data that has
> already been aligned. "By taking data which has already been aligned
> by a heuristic algorithm, we allow the user to optimize where the
> algorithm may have failed," the game creators explain on the site.
>
> All alignments were made available through UCSC Genome Browser and
> contain sections of human DNA which have been speculated to be linked
> to various genetic disorders, such as breast cancer. Every alignment
> is received, analyzed, and stored in a database, where it will
> eventually be re-introduced back into the global alignment as an
> optimization. Players can choose which disease they'd like to work
> on, or be assigned to a random level.
>
> Players don't need to understand (or even care about) phylogenetics
> though. Rather than strings of As, Ts, Cs, and Gs, players align four
> colored squares on a grid. Each row of colors represents a sequence
> from a certain species. Sequences can be moved horizontally and
> spaced out, but not rearranged or deleted. The goal is to line up
> columns of colors that represent alignments between the two or more
> sequences. There will, of course, be gaps in sequences and spots
> where the two rows don't match. The goal is to find the best tradeoff
> between aligning color and creating gaps. Players try to manually
> find the best alignment and beat the computer's original alignment
> score. The first level aligns two sequences, and sequences are added
> as players advance.
>
> Researchers released the game on Monday after testing. They hope the
> create a Facebook, iPhone, and Android application versions of the
> game. Until then, Phylo can be played at http://phylo.cs.mcgill.ca
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 10 Dec 2010 12:20:33 -0500
> From: "John Grehan" <jgrehan at sciencebuff.org>
> Subject: Re: [Taxacom] Phylogenetic Game
> To: "TAXACOM" <taxacom at mailman.nhm.ku.edu>
> Message-ID:
> <26DA12164B238549B6D89A2F2A8EE7990200F0CB at bmsmail.sciencebuff.org>
> Content-Type: text/plain; charset="iso-8859-1"
>
> This just goes to show that molecular phylogenetics is nothing more than a 'game'. Something I have suspected for a long time.
>
> John Grehan
>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Peter Stevens
> Sent: Friday, December 10, 2010 12:02 PM
> To: TAXACOM
> Subject: [Taxacom] Phylogenetic Game
>
> Note that "Players don't need to understand (or even care about)
> phylogenetics."
>
> P.
>
> Subject: Phylogenetics game
>
> December 2, 2010 | A pattern-matching puzzle created by
> bioinformaticians at McGill University lets players sort genetic
> code. The game, called Phylo, takes advantage of the human brain's
> efficiency at recognizing and sorting patterns to tackle multiple
> sequence alignments.
>
> Aligning genetic sequences is traditionally done computationally, but
> what is a huge computational problem, is a bit easier for the human
> brain. "There are some calculations that the human brain does more
> efficiently than any computer can, such as recognizing a face,"
> explained lead researcher J?r?me Waldispuhl of the School of Computer
> Science in a McGill press release. "Recognizing and sorting the
> patterns in the human genetic code falls in that category."
>
> Players don't start from scratch, but instead refine data that has
> already been aligned. "By taking data which has already been aligned
> by a heuristic algorithm, we allow the user to optimize where the
> algorithm may have failed," the game creators explain on the site.
>
> All alignments were made available through UCSC Genome Browser and
> contain sections of human DNA which have been speculated to be linked
> to various genetic disorders, such as breast cancer. Every alignment
> is received, analyzed, and stored in a database, where it will
> eventually be re-introduced back into the global alignment as an
> optimization. Players can choose which disease they'd like to work
> on, or be assigned to a random level.
>
> Players don't need to understand (or even care about) phylogenetics
> though. Rather than strings of As, Ts, Cs, and Gs, players align four
> colored squares on a grid. Each row of colors represents a sequence
> from a certain species. Sequences can be moved horizontally and
> spaced out, but not rearranged or deleted. The goal is to line up
> columns of colors that represent alignments between the two or more
> sequences. There will, of course, be gaps in sequences and spots
> where the two rows don't match. The goal is to find the best tradeoff
> between aligning color and creating gaps. Players try to manually
> find the best alignment and beat the computer's original alignment
> score. The first level aligns two sequences, and sequences are added
> as players advance.
>
> Researchers released the game on Monday after testing. They hope the
> create a Facebook, iPhone, and Android application versions of the
> game. Until then, Phylo can be played at http://phylo.cs.mcgill.ca
>
>
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