Daily Archives: May 18, 2016

Format: Hardcover

This is an excellent overview of current scientific discovery and argument regarding that inheritently common, but innately variable blueprint of 23 pairs of chromosones we all share. Our knowledge of our genes is progressing at a rapid rate, so much so, that by the time I finish writing this sentence, our knowledge of the human genetic code has been updated. If you wish to know what kinds of things are being discovered, this book is a very good place to find it. Matt Ridley devotes each chapter to one of our chromosones-23 in all, and describes some useful dicoveries and speculations regarding each. From such things as the ability to digest lactose, blood groups, cancer suppressors, 'instinct',intelligence, ethics, free will, allergies, aspects of language, ageing, sex, cloning, test tube babies, Mad Cow disease etc, he describes in a clever and clear way the discoveries being made in the field. I would give the book 4 1/2 stars,(but there are no halves in these reviews), as no book is ever perfect, but a point to remember is no understanding of our world, or our genes themselves, is ever perfect either. But we can find pieces to the puzzle, useful and uplifting, and that is what this book is about. Ridleys style is clear and clever, my only quibble is that he displays perhaps just a touch of arrogance, and a subtle air of bias. But give the author his due, an author is entitled to his opinions and leanings, what is important is that he generally makes it clear when he does so. The book is highly recommended for both those familiar with the jargon, and those with enthusiastic minds who wish to learn about it.

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Genome: The Autobiography of a Species in 23 Chapters

Genome size is the total amount of DNA contained within one copy of a single genome. It is typically measured in terms of mass in picograms (trillionths (1012) of a gram, abbreviated pg) or less frequently in Daltons or as the total number of nucleotide base pairs typically in megabases (millions of base pairs, abbreviated Mb or Mbp). One picogram equals 978 megabases.[1] In diploid organisms, genome size is used interchangeably with the term C-value. An organism's complexity is not directly proportional to its genome size; some single cell organisms have much more DNA than humans (see Junk DNA and C-value enigma).

The term "genome size" is often erroneously attributed to Hinegardner,[2] even in discussions dealing specifically with terminology in this area of research (e.g., Greilhuber, 2005[3]). Notably, Hinegardner[2] used the term only once: in the title. The term actually seems to have first appeared in 1968 when Hinegardner wondered, in the last paragraph of his article, whether "cellular DNA content does, in fact, reflect genome size".[4] In this context, "genome size" was being used in the sense of genotype to mean the number of genes. In a paper submitted only two months later (in February 1969), Wolf et al. (1969)[5] used the term "genome size" throughout and in its present usage; therefore these authors should probably be credited with originating the term in its modern sense. By the early 1970s, "genome size" was in common usage with its present definition, probably as a result of its inclusion in Susumu Ohno's influential book Evolution by Gene Duplication, published in 1970.[6]

The genome sizes of thousands of eukaryotes have been analyzed over the past 50 years, and these data are available in online databases for animals, plants, and fungi (see external links). Nuclear genome size is typically measured in eukaryotes using either densitometric measurements of Feulgen-stained nuclei (previously using specialized densitometers, now more commonly using computerized image analysis[7]) or flow cytometry. In prokaryotes, pulsed field gel electrophoresis and complete genome sequencing are the predominant methods of genome size determination. Nuclear genome sizes are well known to vary enormously among eukaryotic species. In animals they range more than 3,300-fold, and in land plants they differ by a factor of about 1,000.[8][9]Protist genomes have been reported to vary more than 300,000-fold in size, but the high end of this range (Amoeba) has been called into question.[by whom?] In eukaryotes (but not prokaryotes), variation in genome size is not proportional to the number of genes, an observation that was deemed wholly counterintuitive before the discovery of non-coding DNA and which became known as the C-value paradox as a result. However, although there is no longer any paradoxical aspect to the discrepancy between genome size and gene number, this term remains in common usage. For reasons of conceptual clarification, the various puzzles that remain with regard to genome size variation instead have been suggested by one author to more accurately comprise a puzzle or an enigma (the C-value enigma). Genome size correlates with a range of features at the cell and organism levels, including cell size, cell division rate, and, depending on the taxon, body size, metabolic rate, developmental rate, organ complexity, geographical distribution, or extinction risk (for recent reviews, see Bennett and Leitch 2005;[8] Gregory 2005[9]). Based on completely sequenced genome data currently (as of April 2009) available, log-transformed gene number forms a linear correlation with log-transformed genome size in bacteria, archea, viruses, and organelles combined whereas a nonlinear (semi-natural log) correlation in eukaryotes (Hou and Lin 2009 [10]). The nonlinear correlation for eukaryotes, although claim of its existence contrasts the previous view that no correlation exists for this group of organisms, reflects disproportionately fast increasing noncoding DNA in increasingly large eukaryotic genomes. Although sequenced genome data are practically biased toward small genomes, which may compromise the accuracy of the empirically derived correlation, and the ultimate proof of the correlation remains to be obtained by sequencing some of the largest eukaryotic genomes, current data do not seem to rule out a correlation.

Genome reduction, also known as Genome degradation, is the process by which a genome shrinks relative to its ancestor. Genomes fluctuate in size regularly, however, genome size reduction is most significant in bacteria.

The most evolutionary significant cases of genome reduction may be the eukaryotic organelles that are derived from bacteria: the mitochondrion and plastid. These organelles are descended from endosymbionts, which can only survive within the host cell and which the host cell likewise needs for survival. Many mitochondria have less than 20 genes in their entire genome, whereas a free-living bacterium generally has at least 1000 genes. Many genes have been transferred to the host nucleus, while others have simply been lost and their function replaced by host processes.

Other bacteria have become endosymbionts or obligate intracellular pathogens and experienced extensive genome reduction as a result. This process seems to be dominated by genetic drift resulting from small population size, low recombination rates, and high mutation rates, as opposed to selection for smaller genomes.

Some free-living marine bacterioplanktons also shows signs of genome reduction, which are hypothesized to be driven by natural selection.[12][13][14]

Obligate endosymbiotic species are characterized by a complete inability to survive external to their host environment. These species have become a considerable threat to human health, as they are often highly capable of evading human immune systems and manipulating the host environment to acquire nutrients. A common explanation for these keen manipulative abilities is the compact and efficient genomic structure consistently found in obligate endosymbionts. This compact genome structure is the result of massive losses of extraneous DNA - an occurrence that is exclusively associated with the loss of a free-living stage. In fact, as much as 90% of the genetic material can be lost when a species makes the evolutionary transition from a free-living to obligate intracellular lifestyle. Common examples of species with reduced genomes include: Buchnera aphidicola, Rickettsia prowazekii and Mycobacterium leprae. One obligate endosymbiont of leafhoppers, Nasuia deltocephalinicola, has the smallest genome currently known among cellular organisms at 112kb.[15] It is important to note, however, that some obligate intracellular species have positive fitness effects on their hosts. (See also mutualists and parasites.)

The reductive evolution model has been proposed as an effort to define the genomic commonalities seen in all obligate endosymbionts.[16] This model illustrates four general features of reduced genomes and obligate intracellular species:

Based on this model, it is clear that endosymbionts face different adaptive challenges than free-living species.

or simply:

In 1991 Drake proposed a rule: that the mutation rate within a genome and its size were inversely correlated.[18] This rule has been found to be approximately correct for DNA viruses and unicellular organisms. Its basis is unknown.

The small size of RNA viruses has been proposed to be locked into a three part relation between replication fidelity, genome size and genetic complexity. The majority of RNA viruses lack an RNA proofreading facility which limits their replication fidelity and hence the genome size. This has also been described as the Eigen paradox.[19]

An exception to the rule of small genome sizes in RNA viruses is found the Nidoviruses. These viruses appear to have acquired a 3-to-5 exoribonuclease (ExoN) which has allowed for an increase in genome size.[20]

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Genome size - Wikipedia, the free encyclopedia

About The Music Genome Project

We believe that each individual has a unique relationship with music no one else has tastes exactly like yours. So delivering a great radio experience to each and every listener requires an incredibly broad and deep understanding of music. That's why Pandora is based on the Music Genome Project, the most sophisticated taxonomy of musical information ever collected. It represents over ten years of analysis by our trained team of musicologists, and spans everything from this past Tuesday's new releases all the way back to the Renaissance and Classical music.

Each song in the Music Genome Project is analyzed using up to 450 distinct musical characteristics by a trained music analyst. These attributes capture not only the musical identity of a song, but also the many significant qualities that are relevant to understanding the musical preferences of listeners. The typical music analyst working on the Music Genome Project has a four-year degree in music theory, composition or performance, has passed through a selective screening process and has completed intensive training in the Music Genome's rigorous and precise methodology. To qualify for the work, analysts must have a firm grounding in music theory, including familiarity with a wide range of styles and sounds.

The Music Genome Project's database is built using a methodology that includes the use of precisely defined terminology, a consistent frame of reference, redundant analysis, and ongoing quality control to ensure that data integrity remains reliably high.

The Music Genome Project is updated on a continual basis with the latest releases, emerging artists, and an ever-deepening collection of catalogue titles.

By utilizing the wealth of musicological information stored in the Music Genome Project, Pandora recognizes and responds to each individual's tastes. The result is a much more personalized radio experience - stations that play music you'll love - and nothing else.

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About The Music Genome Project - Pandora Radio