MachineMachine /stream - tagged with decode https://machinemachine.net/stream/feed en-us http://blogs.law.harvard.edu/tech/rss LifePress therourke@gmail.com <![CDATA[The ENCODE delusion]]> http://scienceblogs.com/pharyngula/2012/09/23/the-encode-delusion

I can take it no more. I wanted to dig deeper into the good stuff done by the ENCODE consortium, and have been working my way through some of the papers (not an easy thing, either: I have a very high workload this term), but then I saw this declaration from the Electronic Frontier Foundation.

On September 19, the Ninth Circuit is set to hear new arguments in Haskell v. Harris, a case challenging California’s warrantless DNA collection program. Today EFF asked the court to consider ground-breaking new research that confirms for the first time that over 80% of our DNA that was once thought to have no function, actually plays a critical role in controlling how our cells, tissue and organs behave.

I am sympathetic to the cause the EFF is fighting for: they are opposing casual DNA sampling from arrestees as a violation of privacy, and it is. The forensic DNA tests done by police forces, however, do not involve sequencing the DNA, but only look at the arrangement of known variable stretches of repetitive DNA by looking at just the length of fragments cut by site-specific enzymes; they can indicate familial and even to some degree ethnic relationships, but not, as the EFF further claims, “behavioral tendencies and sexual orientation”. Furthermore, the claim that 80% of our genome has critical functional roles is outrageously bad science.

This hurts because I support the legal right to genetic privacy, and the EFF is trying to support it in court with hype and noise; their opposition should be able to easily find swarms of scientists who will demolish that argument, and any scientifically knowledgeable judge should be able to see right through the exaggerations (maybe they’re hoping for an ignorant judge?). That conclusion, that 80% of the genome is critical to function, is simply false, and it’s the notorious dishonest heart of ENCODE’s conclusions.

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Tue, 25 Sep 2012 03:41:00 -0700 http://scienceblogs.com/pharyngula/2012/09/23/the-encode-delusion
<![CDATA[Biosemiotics: Searching for meanings in a meadow]]> http://www.newscientist.com/mobile/article/mg20727741.200-biosemiotics-searching-for-meanings-in-a-meadow.html

Are signs and meanings just as vital to living things as enzymes and tissues? Liz Else investigates a science in the making EVERY so often, something shows up on the New Scientist radar that we just can't identify easily. Is it a bird? Is it a plane? Is it a brand new type of flying machine that we are going to have to study closely? That was our reaction when we first heard about a small conference held in June at the philosophy department of the Portuguese Catholic University in Braga. There, a group of biologists, neuroscientists, philosophers, information technologists and other scholars from all over the world gathered to discuss some revolutionary ideas for developing the hitherto obscure field of biosemiotics.

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Fri, 27 Aug 2010 01:08:00 -0700 http://www.newscientist.com/mobile/article/mg20727741.200-biosemiotics-searching-for-meanings-in-a-meadow.html
<![CDATA["Lost" Languages to Be Resurrected by Computers?]]> http://news.nationalgeographic.com/news/2010/07/100719-science-technology-computers-lost-languages-translate-bible-hebrew/

A new computer program has quickly deciphered a written language last used in Biblical times—possibly opening the door to "resurrecting" ancient texts that are no longer understood, scientists announced last week.

Created by a team at the Massachusetts Institute of Technology, the program automatically translates written Ugaritic, which consists of dots and wedge-shaped stylus marks on clay tablets. The script was last used around 1200 B.C. in western Syria.

Written examples of this "lost language" were discovered by archaeologists excavating the port city of Ugarit in the late 1920s. It took until 1932 for language specialists to decode the writing. Since then, the script has helped shed light on ancient Israelite culture and Biblical texts.

(Related: "Oldest Hebrew Text Is Evidence for Bible Stories?")

Using no more computing power than that of a high-end laptop, the new program compared symbol and word frequencies and patterns in Ugaritic with those of a known language, in this

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Tue, 20 Jul 2010 03:56:00 -0700 http://news.nationalgeographic.com/news/2010/07/100719-science-technology-computers-lost-languages-translate-bible-hebrew/
<![CDATA[Plato's stave: academic cracks philosopher's musical code]]> http://www.guardian.co.uk/world/2010/jun/29/plato-mathematical-musical-code

It may sound like the plot of a Dan Brown novel, but an academic at the University of Manchester claims to have cracked a mathematical and musical code in the works of Plato.

Jay Kennedy, a historian and philosopher of science, described his findings as "like opening a tomb and discovering new works by Plato."

Plato is revealed to be a Pythagorean who understood the basic structure of the universe to be mathematical, anticipating the scientific revolution of Galileo and Newton by 2,000 years.

Kennedy's breakthrough, published in the journal Apeiron this week, is based on stichometry: the measure of ancient texts by standard line lengths. Kennedy used a computer to restore the most accurate contemporary versions of Plato's manuscripts to their original form, which would consist of lines of 35 characters, with no spaces or punctuation. What he found was that within a margin of error of just one or two percent, many of Plato's dialogues had line lengths based on round multiples of twel

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Tue, 20 Jul 2010 02:45:00 -0700 http://www.guardian.co.uk/world/2010/jun/29/plato-mathematical-musical-code