{"id":10,"date":"2007-05-24T23:51:00","date_gmt":"2007-05-24T23:51:00","guid":{"rendered":"http:\/\/occamstypewriter.org\/vwxynot\/2007\/05\/24\/science-is-a-symphony\/"},"modified":"2007-05-24T23:51:00","modified_gmt":"2007-05-24T23:51:00","slug":"science-is-a-symphony","status":"publish","type":"post","link":"https:\/\/occamstypewriter.org\/vwxynot\/2007\/05\/24\/science-is-a-symphony\/","title":{"rendered":"Science is a Symphony"},"content":{"rendered":"

I came into work this morning thinking that it was about time I found an interesting paper to summarise here. My inbox contained table of contents alerts from various journals, so I ignored the strictly work-related ones and went straight for the interesting stuff. Well, I felt like a kid in a candy store this morning. Thank you Genome Biology<\/em> <\/a>and Trends in Genetics<\/em> <\/a>for an excellent half hour of abstract reading. Several papers have been printed out and are duly awaiting some spare time with a nice cup of tea.<\/p>\n

All that can wait though, because one paper really caught my eye this morning. Take a look <\/a>at the wonderful \u201cConversion of amino-acid sequence in proteins to classical music: search for auditory patterns\u201d by Rie Takahashi and Jeffrey Miller of UCLA.<\/p>\n

Hey, I like searching for patterns in genomic sequences. I love music. And now I love finding MP3s in the Supplemental Information section of online scientific journals.<\/p>\n

The first audio clip sounded distinctly weird. Each of the 20 amino acids found in a stretch of the human Thymidylate Synthase A protein was assigned an individual note. The result is a random assortment of evenly spaced notes.<\/p>\n

The next clip assigns each amino acid a unique 3-note chord. Amino acids with similar chemical properties were given different versions of the same chord – basically different arrangements of the same notes, in the same way that similar amino acid molecules might have different rearrangements of the same atoms. The derived music whips along at a cracking (albeit monotonous) pace, and even has some quite pleasant moments.<\/p>\n

Finally, rhythm was introduced by looking at which specific DNA sequence was used to encode each amino acid. Some amino acids can be encoded by 2 or more different codons (stretches of 3 DNA base pairs), and each codon is used with a different frequency in the human genome. Amino acids encoded by the most common codons were assigned longer note lengths. At this point we\u2019re getting (slightly) closer to something that sounds like real, human music. It might have rhythm, but it ain’t got no soul.<\/p>\n

The researchers\u2019 website <\/a>contains some further examples of protein sequences converted to music. I was particularly interested in listening to the c-Jun protein clip, as I spent a lot of time and effort working on this protein during my postgraduate research. Much like my PhD experience, the music was frustrating to sit through with the occasional enjoyable patch. It ended very abruptly, which may represent submitting a thesis and getting on a plane to Canada. Who knows? I\u2019m no expert music critic.<\/p>\n

Takahashi and Miller hope that their work will open up the field of genomics to visually impaired researchers and make genomics more attractive to a wider audience, especially young people. This paper could definitely be converted into a fun classroom activity, perhaps comparing the music derived from the same protein in different species. I look forward to hearing clips from the next stage of their work, with different instruments representing DNA sequences with different roles in the genome.<\/p>\n

I\u2019m sure that some creationists will jump on this paper and claim that it proves some kind of design in the human genome sequence. This is a fun study, but if there does happen to be an Intelligent Composer out there, may I suggest some more music lessons? <\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

I came into work this morning thinking that it was about time I found an interesting paper to summarise here. My inbox contained table of contents alerts from various journals, so I ignored the strictly work-related ones and went straight … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":10,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[11,12,13,3],"tags":[],"class_list":["post-10","post","type-post","status-publish","format-standard","hentry","category-journal-club","category-music","category-original-research","category-science"],"_links":{"self":[{"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/posts\/10","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/users\/10"}],"replies":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/comments?post=10"}],"version-history":[{"count":0,"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/posts\/10\/revisions"}],"wp:attachment":[{"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/media?parent=10"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/categories?post=10"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/occamstypewriter.org\/vwxynot\/wp-json\/wp\/v2\/tags?post=10"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}