Artistic value in scientific results, a means for science communication creative kings 10-mar-2009 ...

artistic value in scientific results,a means for science communication

creative king’s10-mar-2009

http://www.kcl.ac.uk/schools/pse/bioinform/

[email protected]™ and a

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structure

• BIOLOGY & BIOINFORMATICS• visualization & interpretation of scientific results• who are we, the centre for bioinformatics• a crash course in biology• a movie: the inner life of a cell

• CREATIVITY IN SCIENCE• creativity, definitions• importance of creativity, co-occurrence of terms• artists on science, scientists on art• science communication, good examples

• ARTISTIC VALUE IN SCIENTIFIC RESULTS• importance of science?• neurobiology of perception• genome evolution, a case study• the importance of scales, and the media



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structure






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The storage, analysis and distribution of biological information, usually at the molecular but also at the supra-molecular levels of organization

A ‘dirty’ word:• more traditionally…

• sequence analysis• structure prediction• molecular evolution

• and more to the definition…

• data engineering [storage]• computational biology

[analysis]• network services [distribution]

Overlaps with…• all the way from theoretical

biology…• …to medical informatics and any

other -matics or -omics• driving force behind genomics

what is bioinformatics?

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kcbiking’s college london centre for bioinformatics

structural genomics• fraternali

functional genomics• blanc

statistical genetics• schlitt

systems biology• tsoka

comparative genomics• ouzounis

http://www.kcl.ac.uk/schools/pse/bioinform/

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School of Physical Sciences and Engineering

Professor Christos Ouzounis

Dr Sophia Tsoka

Paul Keeling, Sr Admin Officer, strategic planning

MRC Centre for Developmental Neurobiology

Dr Eric Blanc

Randall Division of Cell and Molecular Biophysics

Dr Franca Fraternali

Department of Medical and Molecular Genetics

Dr Thomas Schlitt

Department of Computer Science

Professor Maxime Crochemore

Professor Mark Harman

Professor Costas Iliopoulos

Dr Kathleen Steinhöfel

Division of Engineering

Dr Mark Miodownik

School of Medicine

Professor Frank Nestle

Dr Rebecca Oakey

Dr Roli Roberts

Dr Reiner Schulz

Institute of Psychiatry

Professor Simon Lovestone

MRC Centre for Developmental Neurobiology

Dr David Chambers

Mathematics Department

Professor Ton Coolen

Visiting Professors

Ben Blencowe, University of Toronto

Peter D. Karp, SRI International, Benlo Park CA

Nikos Kyrpides, Joint Genome Institute, Berkeley CA

Arthur Lesk, Penn State University, University Park PA

Alfonso Valencia, CNIO Madrid, Spain

core and associate members

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a visual summary of our work





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the very basics

the biological hierarchy• populations• organisms• systems• organs• tissues• cell types• cells• subcellular compartments• macromolecular complexes• macromolecules• small molecules• atoms• …

http://www.ehponline.org/members/2007/10373/fig1.jpg



http://kentsimmons.uwinnipeg.ca/cm1504/Image48.gif

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from DNA to gene

measuring length:

Units of length for DNA moleculesBecause DNA is double-stranded, the lengths of molecules are described as so many base pairs (bp).A kilobase pair (kb) is 103 bp and a megabase pair (Mb) is 106 bp.A gigabase pair (Gb) is 109 Mb.

In summary:1 kb = 1000 bp1 Mb = 1000 kb = 1 000 000 bp1 Gb = 1000 Mb = 1 000 000 kb = 1 000 000 000 bp

Typically, genome sizes range from Mbs to Gbs - and they contain between 1,000 and 100,000 genes

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=genomes.box.5275

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a gene in ascii : acgt

ATGCCCGTTGCCCACGTTGCCTTGCCCGTTCCGCTTCCTCGTACCTTTGACTATCTGCTGCCAGAAGGCATGACGGTTAAAGCTGGGTGTCGCGTGCGCGTGCCGTTTGGCAAACAGCAGGAGCGCATCGGGATTGTGGTATCAGTTAGCGATGCCAGCGAACTGCCGCTCAATGAGCTAAAAGCGGTAGTCGAAGTGCTGGATAGTGAGCCGGTGTTTACTCACTCCGTCTGGCGATTGCTGCTATGGGCGGCAGATTACTATCATCATCCGATTGGCGATGTGCTGTTTCATGCCTTGCCGATTTTACTACGCCAGGGGCGGCCTGCGGCGAACGCGCCGATGTGGTACTGGTTTGCCACTGAACAAGGCCAGGCGGTGGATCTGAACAGCCTGAAACGCTCCCCCAAGCAACAACAGGCGCTGGCGGCGTTACGGCAAGGCAAAATCTGGCGCGACCAGGTCGCCACGCTCGAATTTAATGATGCCGCGTTGCAGGCGCTACGCAAAAAAGGTCTGTGTGATTTAGCAAGTGAAACACCAGAGTTTAGCGACTGGCGAACGAACTATGCCGTTTCTGGTGAGCGGTTGCGATTGAATACCGAACAGGCCACCGCCGTTGGCGCAATTCATAGCGCGGCAGATACTTTTTCTGCCTGGCTGCTGGCGGGCGTTACCGGTTCCGGTAAAACGGAGGTTTATCTCAGCGTACTGGAAAACGTGCTCGCTCAGGGCAAACAGGCGCTGGTGATGGTGCCGGAAATCGGCCTGACACCGCAAACTATCGCCCGTTTTCGTGAACGTTTTAATGCCCCCGTGGAAGTTCTGCATTCCGGCCTGAACGACAGCGAGCGTCTTTCGGCGTGGCTGAAAGCGAAAAATGGTGAGGCGGCGATTGTGATCGGCACCCGCTCCGCGCTGTTTACGCCGTTTAAAAATCTCGGCGTGATTGTCATTGATGAAGAGCACGACAGCTCCTACAAGCAGCAGGAAGGCTGGCGCTATCATGCCCGCGACCTGGCGGTGTATCGTGCGCACAGCGAGCAAATCCCGATTATTCTTGGCTCCGCAACGCCCGCGCTGGAAACGTTATGCAACGTCCAGCAGAAAAAATACCGCCTGCTGCGCCTGACCCGTCGGGCAGGGAATGCGCGTCCGGCAATTCAACATGTGCTGGATTTAAAAGGTCAGAAGGTGCAGGCAGGTCTGGCTCCGGCGTTAATCACTCGTATGCGCCAGCATTTACAGGCTGATAACCAGGTCATTCTCTTTCTTAACCGCCGTGGCTTTGCGCCTGCACTGCTGTGCCACGACTGTGGCTGGATTGCCGAATGCCCACGTTGCGATCACTACTACACGCTGCATCAGGCGCAGCACCATCTGCGCTGCCACCACTGTGACAGTCAGCGTCCGGTGCCGCGCCAGTGCCCTTCCTGCGGTTCCACGCACCTGGTCCCCGTGGGGCTGGGCACCGAACAGCTTGAACAGACGCTCGCGCCGTTGTTCCCCGGCGTGCCCATTTCTCGTATCGACCGCGATACCACCAGCCGCAAAGGGGCGCTGGAACAGCAACTGGCAGAAGTACATCGCGGCGGCGCGCGGATTTTGATTGGTACACAAATGCTGGCGAAAGGTCACCATTTCCCGGATGTGACGCTGGTTGCATTACTGGACGTGGACGGCGCGCTGTTTTCTGCCGATTTTCGCTCGGCAGAGCGTTTCGCTCAGCTTTACACCCAGGTCGCCGGTCGTGCCGGGCGTGCGGGTAAACAGGGCGAAGTGGTGCTGCAAACGCACCATCCGGAACATCCTCTGTTGCAAACGTTGCTCTATAAAGGCTACGACGCCTTTGCCGAACAGGCGCTGGCTGAGCGGCGAATGATGCAGCTACCGCCGTGGACCAGCCATGTGATTGTGCGTGCGGAAGATCATAACAATCAGCACGCGCCATTGTTCCTGCAACAACTGCGTAATCTGATCCTCTCCAGCCCACTGGCAGACGAGAAACTGTGGGTTCTCGGTCCGGTTCCGGCTCTGGCACCTAAACGTGGCGGTCGCTGGCGCTGGCAGATATTGTTGCAGCACCCTTCCCGCGTGCGCTTGCAACACATCATTAACGGTACGCTGGCGCTCATCAATACAATACCGGATTCCCGTAAGGTGAAATGGGTGCTGGATGTTGATCCGATTGAGGGTTAA



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a protein in ascii : acdefghiklmnpqrstvwy

MPVAHVALPVPLPRTFDYLLPEGMTVKAGCRVRVPFGKQQERIGIVVSVSDASELPLNELKAVVEVLDSEPVFTHSVWRLLLWAADYYHHPIGDVLFHALPILLRQGRPAANAPMWYWFATEQGQAVDLNSLKRSPKQQQALAALRQGKIWRDQVATLEFNDAALQALRKKGLCDLASETPEFSDWRTNYAVSGERLRLNTEQATAVGAIHSAADTFSAWLLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGEAAIVIGTRSALFTPFKNLGVIVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALETLCNVQQKKYRLLRLTRRAGNARPAIQHVLDLKGQKVQAGLAPALITRMRQHLQADNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQHHLRCHHCDSQRPVPRQCPSCGSTHLVPVGLGTEQLEQTLAPLFPGVPISRIDRDTTSRKGALEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALLDVDGALFSADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLYKGYDAFAEQALAERRMMQLPPWTSHVIVRAEDHNNQHAPLFLQQLRNLILSSPLADEKLWVLGPVPALAPKRGGRWRWQILLQHPSRVRLQHIINGTLALINTIPDSRKVKWVLDVDPIEG



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many genomes have been deciphered



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domains of lifethere are three known domains / types of cells: archaea, bacteria, eukarya



http://tainano.com/Molecular%20Biology%20Glossary.files/image015.gif



http://www.biologyreference.com/Ar-Bi/Archaea.html



http://www.garlandscience.com/textbooks/0815341059.asp



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genome trees

better trees are derived from whole-genome comparisons

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the eukarya, useukarya are very diverse !



http://wiki.cotch.net/upload/5/5f/Eukaryoticlife.jpg

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structure






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creativity



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creativity, co-occurrence terms





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creativity barometer

education role of the leader

brain innovation leadership innovation manageme

nt

intelligence depression madness mental illness

1

10

100

1000

10000

100000

25300

8610 8270

3120

481 444 421293

233 229

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creativity in society



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visual arts in sciences

QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.



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artists on science, scientists on art

• a relevant dialogue, e.g. "Artists on science: scientists on art." Special section in Nature, 17 March 2005, pages 293-323

• distinction of “two cultures”, science & technology vs. art & poetry is somewhat outdated

• “… There is an economy of words and beauty of concept in poetry that is always found in the best science” (Garfield, 1989)• Creativity is a modern concept. Term was not coined until 1875, when it was used to refer to the poetic imagination.



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a piece of art from a famous scientist

“It may seem unusual to include Leonardo da Vinci in a list of paleontologists and evolutionary biologists. Leonardo was and is best known as an artist, the creator of such masterpieces as the Mona Lisa, Madonna of the Rocks, and The Last Supper. Yet Leonardo was far more than a great artist: he had one of the best scientific minds of his time. He made painstaking observations and carried out research in fields ranging from architecture and civil engineering to astronomy to anatomy and zoology to geography, geology and paleontology.”



http://www.ucmp.berkeley.edu/history/vinci.html

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the importance of science communication



http://www.auburn.edu/~mathest/nufs2000_clip_image002_0000.jpg

http://www.flickr.com/photos/rafaerts/2817098501/





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structure






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the importance of science?



Science pollPublished: Wednesday, 28 January 2009The public was asked what has the most impact in shaping their futures; 26% said science, putting it ahead of politics, family and religion. When asked to choose which group of people has the most effect on our daily lives, only 3% selected scientists.



http://sciencesowhat.direct.gov.uk/

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neurobiology of perception







Elements of perspective, shadows, transparency, reflections: all understood in terms of visual computations in our brain

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microphotography

http://www.nikonsmallworld.com/

























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a sense of scale

Genomes 377

Genes 1,315,558

Annotations 359,482

Similarities 384,579,409

Phylogenetic profiles

181,986

Families 82,692

Interactions 2,192,019

Pathways > 25,000

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protein classification & similarity graphs



http://bioinformatics.icmb.utexas.edu/lgl/Images/scop_hie_full.jpg



http://bioinformatics.icmb.utexas.edu/lgl/Images/phg.jpg





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more views of the similarity graph



http://bioinformatics.icmb.utexas.edu/lgl/PHN/phn.large.png

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zooming into the unknown













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a sense of scale

Genomes 377

Genes 1,315,558

Annotations 359,482

Similarities 384,579,409

Phylogenetic profiles

181,986

Families 82,692

Interactions 2,192,019

Pathways > 25,000

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ancestral gene content

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1708

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Gene content reconstruction: ancestral states

Both current and ancient genomes• HGT events on

tree

The enigmatic yellow sphere is the universal ancestor

Featured in Wired, Discover etc.

network of life

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net of life, the movie

http://www.nature.com/embor/journal/v8/n10/full/7401074.html

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the importance of scales, and the media• for artists, other scales do not provide typical material• there is a beauty in the microcosm, stunning views that need to be captured

• stunning representations of complex phenomena with artistic value• inaccessible in their usual form to wider communities

• including other scientists, artists and the general public

• these representations (“results”) are abstract notions• they do not correspond to the physical world• they do, however, provide the means for effective science communication

with the appropriate use of media and inter-disciplinary collaborations

• results of complex analyses can have both artistic content and scientific accuracy

Artistic value in scientific results, a means for science communication creative kings 10-mar-2009 ...

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