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Topic: Synonymous or silent substitution

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	The Individualist: Neutral theory of molecular evolution
		Consequently, many potential single-nucleotide changes are in effect "silent" or "unexpressed" (synonymous or silent substitution).
		When an allele carrying one of these new substitutions becomes fixed, the effect is to add a substitution to the sequence of the previously fixed allele.
		According to the mathematics of drift, when looking between two species or two isolated populations, most of their single-nucleotide differences can be assumed to have accumulated at the same rate as individuals with mutations are born.
	www.dadamo.com /wiki/wiki.pl/Neutral_theory_of_molecular_evolution (1384 words)

	Language in India
		Substitution of a word, phrase, or sentence by another is an elementary method which helps students to produce new utterances and to develop speaking skill.
		Substitution of sounds in minimally different words is a common practice in listening exercises to develop auditory discrimination of sounds.
		Substitution of one word or phrase by another in the same slot in a frame is a common practice in speaking exercises at the beginners’ level.
	www.languageinindia.com /april2002/tesolbook.html (20400 words)

	Codon
		There are 64 varieties of codon of which 61 specify the merging of an amino acid into a polypeptide chain while the remaining three are stop codons, also known as termination codons or nonsense codons, that are the signal to stop protein synthesis.
		Most codons have an equivalent alternative, where the substitution of 'silent' nucleotides will not change the encoded amino acid, apart from (in the universal genetic code) Methionine (AUG) and Tryptophan (UGG).
		It is often spoken of "the" codon usage pattern of an organism, but it is rarely true that all of the genes demonstrate the same codon usage patterns.
	www.iscid.org /encyclopedia/Codon (266 words)

	Seed: The Sound of Silence
		Chava Kimchi-Sarfaty and her colleagues at the National Institutes of Health were trying to understand why certain silent mutations occurred with unusual frequency in a gene called multidrug resistance 1 (MDR1), found in human cancer cells.
		This mechanism, which they call "translational pausing," is actually just one of several ways in which silent mutations have very recently been shown to affect protein function—and, more broadly, the fitness of an organism.
		It turns out that silent mutations can also change the stability of mRNA, one of the important intermediates in the transfer of information from DNA to proteins, and disrupt gene splicing, the process by which the DNA that contains genes is trimmed away from the rest of the genome.
	www.seedmagazine.com /news/2007/03/the_sound_of_silence.php (624 words)

	The Causes of Synonymous Rate Variation in the Rodent Genome: Can Substitution Rates Be Used to Estimate the Sex Bias ...
		synonymous mutations on the X chromosome relative to the autosomes,
		synonymous substitution rates might be due to sequence differences.
		, D., C., and G., 1995 Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions.
	www.genetics.org /cgi/content/full/152/2/661 (6263 words)

	CATHOLIC ENCYCLOPEDIA: Evolution
		The concept, therefore, of species according to Holy Scripture, Philosophy, and Science, is by no means a synonymous one for the natural units of the organic world.
		In short, if we disregard observation and experiment on living organisms, it is the historical method alone which can decide the limits of evolution and the succession and genetic relations of the different forms.
		Palæontology is silent likewise about the early history of mammals.
	www.newadvent.org /cathen/05655a.htm (13590 words)

	[No title]
		This is evidenced in their laws, the bulk of which invaders through the centuries have kept, because of the excellence of these Laws18 ; this is evidenced in their artistic expression ; and personal attempts at excellence is a big part of the ways of people who understand and believe in reincarnation.
		Three reasons for keeping silent: against saying the thing one ought not, against speaking in the way one ought not, and against speaking in the place one ought not.
		A workable modern substitution is the pledging of ones' assets.
	wolf.mind.net /library/celtic/triads/triads.htm (12113 words)

	Alphabetical Command List for AutoHotkey
		Sends a message to a window or control and waits for acknowledgement.
		Makes Send synonymous with SendInput or SendPlay rather than the default (SendEvent).
		Also makes Click and MouseMove/Click/Drag use the specified method.
	www.autohotkey.com /docs/commands.htm (2285 words)

	Theosophy World — Home Page
		They were written to appeal to the 'highest minds', who in turn, as far as possible, would disseminate their content to others, i.e the grand ideas would percolate down and so influence all society.
		A consequence of the virtual substitution of the original literature by that of the second generation writers has meant that there has been very little follow-up material in the HPB/Masters vein.
		The other secrets, of the Mysteries, perhaps, only come to those whose lips are already sealed against their betrayal.
	www.theos-world.com /archives/show.php?NAME=tw199706&PATH=txt&DESC=Jun... (13452 words)

	The Language of Thought Hypothesis
		LOTH is a full-blown attempt to give a naturalist answer to the third question, an attempt to solve at least part of the problem underlying the second one, and is almost completely silent about the first.
		As indicated previously, LOTH is almost completely silent about consciousness and the problem of qualia, the third mystery in Fodor's list in the quote above.
		The level of analysis to which the designer's remark belongs describes features of the program that are, in an entirely innocent way, emergent properties of the computational processes that have "engineering reality." I see no reason to believe that the relation between belief-talk and psychological talk will be any more direct.
	plato.stanford.edu /entries/language-thought (12152 words)

	CM Series
		The children were astonishing to me; they were persons of generous impulses and sound judgment, of great intellectual aptitude, of imagination and moral insight.
		But, it will be said, reading or hearing various books read, chapter by chapter, and then narrating or writing what has been read or some part of it,––all this is mere memory work.
		The moment has come for a decision; we have placed our faith in 'civilisation,' have been proud of our progress; and of the pangs that the War has brought us, perhaps none is keener than that caused by the utter breakdown of the civilisation which we have held to be synonymous with education.
	www.amblesideonline.org /CM/6_0_1_book1.html (3811 words)

	Malaria. Plasmodium falciparum. Synonymous Mutations and Low complexity Segments (Site not responding. Last check: 2007-11-01)
		This assumes that synonymous mutations are adaptively neutral, and hence reflect the ‘
		17 Saul, A. (1999) Circumsporozoite polymorphisms, silent mutations and the evolution of Plasmodium falciparum.
		30 Sharp, P.M. and Li, W.-H. (1987) The rate of synonymous substitution in eubacterial genes is inversely related to codon usage bias.
	mail.queensu.ca /~forsdyke/pfalcip01.htm (8941 words)

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