Biological Information: New Perspectives

Paul Giem Lectures

Part 1: http://youtu.be/vg_xp0dRUdM?list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ
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The book "Biological Information: New Perspectives" was published in 2013, two years after the symposium at Cornell University of the same name. The general introduction to the book (an overview) will be reviewed, along with the controversy over its publication.

1. Marks, R. J. II et al. 2013. Biological Information: New Perspectives. Hackensack, NJ: World Scientific Publishing Co. Pte. Ltd. - General Introduction available at http://www.worldscientific.com/doi/su... - Book available in sections at http://www.worldscientific.com/worlds...
2. For the anti-book perspective, see http://pandasthumb.org/archives/2012/... and http://www.antievolution.org/cgi-bin/...
3. For the pro-book perspective, see http://www.evolutionnews.org/2013/08/... and http://www.evolutionnews.org/2013/08/...

Part 2: Biological Information - What is It?

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In the book "Biological Information: New Perspectives" the chapter entitled "Biological Information - What is It?" discusses 3 different scientific definitions of information and then introduces the concept of Universal Information, which corresponds more closely to what most people mean when they use the word "information".

1. Marks, R. J. II et al. 2013. Biological Information: New Perspectives. Hackensack, NJ: World Scientific Publishing Co. Pte. Ltd. - Chapter available at http://www.worldscientific.com/doi/pd... - Book available in sections at http://www.worldscientific.com/worlds...

Part 3: Reverse Conservation

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In the book "Biological Information: New Perspectives" the chapter entitled "A General Theory of Information Cost Incurred by Successful Search" discusses the source of biological information and shows that a search for information has to be informed already in order to find and recognize that information. Information can be destroyed, but not created outside of intelligence.

1. Marks, R. J. II et al. 2013. Biological Information: New Perspectives. Hackensack, NJ: World Scientific Publishing Co. Pte. Ltd. - Chapter available at http://www.worldscientific.com/doi/pd... - Book available in sections at http://www.worldscientific.com/worlds...

Part 4: Overlapping Codes

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Part 5: Tierra

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In the book "Biological Information: New Perspectives" the chapter entitled "Tierra: The Character of Adaptation" discusses one of the more sophisticated computer models of evolution and its failure to achieve the results anticipated by its creator.

1. Marks, R. J. II et al. 2013. Biological Information: New Perspectives. Hackensack, NJ: World Scientific Publishing Co. Pte. Ltd. - Chapter available at http://www.worldscientific.com/doi/pd... - Book available in sections at http://www.worldscientific.com/worlds...

Part 6: Entropy, Evolution and Open Systems

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In the book "Biological Information: New Perspectives" the chapter entitled "Entropy, Evolution and Open Systems" discusses the question of whether the Second Law of Thermodynamics can be circumvented simply by having an open system, or whether there are other requirements regarding that open system.

1. Marks, R. J. II et al. 2013. Biological Information: New Perspectives. Hackensack, NJ: World Scientific Publishing Co. Pte. Ltd. - Chapter available at http://www.worldscientific.com/doi/pd... - Book available in sections at http://www.worldscientific.com/worlds...

Part 7: Information and Thermodynamics in Living Systems

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In the book "Biological Information: New Perspectives" the chapter entitled "Information and Thermodynamics in Living Systems" discusses the role of machines in creating local decreases in entropy in an open system and suggests that they are required; and this requirement implies intelligence.

1. Marks, R. J. II et al. 2013. Biological Information: New Perspectives. Hackensack, NJ: World Scientific Publishing Co. Pte. Ltd. - Chapter available at http://www.worldscientific.com/doi/pd... - Book available in sections at http://www.worldscientific.com/worlds...

Part 8: Biological Information - Not Junk After All

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In the book "Biological Information: New Perspectives" the chapter entitled "Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information" discusses the various functions of DNA and finds that non-functional DNA is a small minority.

1. Marks, R. J. II et al. 2013. Biological Information: New Perspectives. Hackensack, NJ: World Scientific Publishing Co. Pte. Ltd. - Chapter available at http://www.worldscientific.com/doi/pd... - Book available in sections at http://www.worldscientific.com/worlds...

Part 9: Overlapping Genetic Codes

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In the book "Biological Information: New Perspectives" Chapters 6 and 9 (at least) argue that stretches of DNA can have multiple functions encoded into them. We will partially evaluate the strength of the evidence behind that argument.

1. Marks, R. J. II et al. 2013. Biological Information: New Perspectives. Hackensack, NJ: World Scientific Publishing Co. Pte. Ltd. - Book available in sections at http://www.worldscientific.com/worlds...
2. Kapranov P., et al. 2005. Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997. Available at http://www.ncbi.nlm.nih.gov/pmc/artic...
3. Birney E., et al. (Encode Project Consortium) 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816. Available at http://www.nature.com/nature/journal/...
4. Itzkovitz S., Hodis E., Sega E. 2010. Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589. Available at http://genome.cshlp.org/content/early...
5. He H., et al. 2007. Mapping the C. elegant noncoding transcriptome with a whole genome tiling microarray. Genome Res 17:1471-1477. Available at http://genome.cshlp.org/content/17/10...
6. http://www.mcld.co.uk/hiv/?q=HIV%20ge...
7. http://nsmn1.uh.edu/dgraur/niv/sabath...

Part 10: Criticizing ENCODE 

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In the book "Biological Information: New Perspectives" Chapter 9 argues that the vast majority of the genome is functional. In 2012 the ENCODE consortium published over 30 papers and argued that more than 80% of the human genome had at least one biochemical function. Dan Graur et al. have offered a critique. We review that critique.

1. Marks, R. J. II et al. 2013. Biological Information: New Perspectives. Hackensack, NJ: World Scientific Publishing Co. Pte. Ltd. - Chapter available at http://www.worldscientific.com/doi/pd... - Book available in sections at http://www.worldscientific.com/worlds...
2. The ENCODE project consortium, 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74. Available at http://www.nature.com/nature/journal/....
3. Graur, D. et al. 2013. On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol (2013) doi: 10.1093/gbe/evt028. Available at http://gbe.oxfordjournals.org/content...
4. Ohno, S. 1972. So much "junk" DNA in our genome. Evolution of genetic systems. Brookhaven symposia in biology 23: 366-370. Available at http://www.junkdna.com/ohno.html
5. http://judgestarling.tumblr.com/post/...

Part 11: Purifying Selection

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In the book "Biological Information: New Perspectives" the chapter entitled "Can Purifying Natural Selection Preserve Biological Information?" tries to answer that question using a program called Mendel's Accountant. The answer appears to be no.

1. Marks, R. J. II et al. 2013. Biological Information: New Perspectives. Hackensack, NJ: World Scientific Publishing Co. Pte. Ltd. - Chapter available at http://www.worldscientific.com/doi/pd... - Book available in sections at http://www.worldscientific.com/worlds...
2. http://mendelsaccount.sourceforge.net

Biological Information: New Perspectives

Paul Giem Lectures