Data, Information, and all that....

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DNAunion: Uhm, there are reasons to think that mutations aren’t truly random: for example, genomes can have hotspots where mutations occur at a higher rate. In such genomes, because the mutations are not evenly distributed, technically, they are not random. There are plenty of debates at sites such as this one that are based on what the word random really means and I didn’t want to get bogged down in such.

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Peter: I agree that we shouldn't get borged down on this one ..

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And yet you responded as if I were wrong!?!?

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Peter: You don't need even distribution (spatially) for the mutations to be random ...

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Why are you addressing a statement I didn't make?Now, let’s take a look to see if uneven distribution can legitimately be taken to mean that something is not random.First, from Webster’s Ninth New Collegiate Dictionary:

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random b: being or relating to a set or to an element of a set each of whose elements has equal probability of occurrence ; also : characterized by procedures designed to obtain such sets or elements <~ sampling>

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and then

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Pincus and Singer built on the observation that all possible digits are represented about equally in a perfectly random stream of numbers. For example, the binary sequences 01101100 and 01010101 — each with four 1s and four 0s — pass this test. But the researchers also noted that when the digits are taken two at a time, a random sequence should have an equal number of all possible pairs: 00, 01, 10, and 11, in this case. (New Test Sized Up Randomness, Charles Seife, Science, Volume 276, Number 5312, Issue of 25 Apr 1997, p532)

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Here’s another.

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Nat Genet. 2002 Oct;32(2):296-9. Epub 2002 Sep 16.

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An initiation site for meiotic crossing-over and gene conversion in the mouse.

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Guillon H, de Massy B.

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Institut de Genetique Humaine, UPR1142/CNRS, 141 rue de la Cardonille 34396 Montpellier cedex 05, France.

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During meiosis, the reductional segregation of homologous chromosomes at the first meiotic division requires reciprocal exchange (crossing over) between homologs. The number of crossovers is tightly regulated (one to two per homolog in mice), and their distribution in the genome is not random-recombination 'hot' and 'cold' regions can be identified. We developed a molecular assay to study these events directly in mouse germ cells. This analysis was developed with reference to the proteosome subunit beta type 9 (Psmb9, previously called Lmp2) hot-spot region identified through genetic analysis. Here we show that this hot spot is an initiation site of meiotic recombination on the basis of two observations: (i) crossover density is maximal in an interval of 210 bp and decreases on both sides of this region; (ii) a high frequency of gene conversion is found in the region of highest crossover density. We then used this strategy to carry out the first temporal analysis of meiotic recombination in mouse spermatogenesis and demonstrate that crossover events occur during the pachytene stage of meiotic prophase. (emphasis added, An initiation site for meiotic crossing-over and gene conversion in the mouse - PubMed)

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And another that links nonrandom to uneven distribution

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A highly statistically significant nonrandom sequence distribution was observed readily in the pool of selected molecules (Table 1) but not in the control samples (data not shown). Although samples containing the consensus 5'-(N)ARAR are a subset of those containing 5'-(N)A, their observed frequency in the pool of the latter sequence (12/45) was much higher than expected by random distribution ( 2 = 30), suggesting that they were selected independently. Furthermore, only 11 mutations at 2 sites were scored where C was the nearest neighbor on both sides of the mutations, and 2 mutations at one site were surrounded by Ts (representing random distribution in the first case and significant underrepresentation in the second) (Just a moment...)

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and

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Spontaneous deaminations are not found in random locations. It is clear that HOTSPOTS exist at which the frequencies of mutation are much greater than usual. (Page Not Found | We cannot find your page (404 Error) | Memorial University of Newfoundland)

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So if something’s distribution is far from being equal, it can correctly be said to be nonrandom. Thus, it can be correctly stated that genomes with hotspots — mutations that are clearly not evenly distributed throughout the genome - have mutations that are not truly random.But, by all means, let's not get bogged down with this! :-)[This message has been edited by DNAunion, 03-24-2004]

You know the question now so why not answer it ? I know I it put it very clearly last time, so quit stalling. I'll ask it again if you wantWhere do you think the information that was in the common ancestor cell(s) came from?That is the question you have not answered - notice the past tense. If you want to answer it this time, then great! If not then get back under your bridge and wait for a bigger billy goat.

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DNAunion: See, you're confused. You claim that you didn't ask me what you did in fact ask, and you also claim that you asked me what you in fact did not.

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Anybody get the feeling DNAunion didn't get enough attention as a child?regards
Esteban "Losing Respect" Hambre

Just curious: By extension, when I go to the Indian casino up the road and shoot craps, does the fact that the craps roll only happens at the craps table and never in the lobby or by the Bingo games - that is to say, not "equally spacially distributed" - mean that the craps roll is nonrandom?(Ah, but of course, you're talking about DNA and not casinos. Guess I might as well say "ah" in preparation for you to jump down my throat again. Prove me wrong, maybe?)

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DNAunion: So if something’s distribution is far from being equal, it can correctly be said to be nonrandom. Thus, it can be correctly stated that genomes with hotspots — mutations that are clearly not evenly distributed throughout the genome - have mutations that are not truly random.

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Crashfrog: Just curious: By extension, when I go to the Indian casino up the road and shoot craps, does the fact that the craps roll only happens at the craps table and never in the lobby or by the Bingo games - that is to say, not "equally spacially distributed" - mean that the craps roll is nonrandom?

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A "counter" so ridiculous it doesn't deserve my - or anyone else's - time.[This message has been edited by DNAunion, 03-24-2004]

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Oook: You know the question now so why not answer it ?

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And you now know you were the cause of the miscommunication, so why not admit it?

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Oook: I know I it put it very clearly last time...

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Why not the FIRST time?

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Oook: ... so quit stalling. I'll ask it again if you want

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Where do you think the information that was in the common ancestor cell(s) came from?

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So why didn't you ask that originally? Too hard for you to think of? Too lazy?Oh, and I have a surprise for you when I do answer that question.

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Oook: That is the question you have not answered

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That is the question you didn't ask when you pretended that you had.

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Oook: - notice the past tense.

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You finally got something right! Hooray!

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Oook: If you want to answer it this time, then great!

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Okay, so what's my position on how the information got into the common ancestor...undirected evolution, of course. The LUCA is believed to have existed long after life originated: long after "random" mutation and natural selection were operating on living entities.Gee, did you ask the wrong question again! LOL!

Am I to presume that you say that simply because you don't have an answer? Because it looks that way. Why else would a simple question be responded to with ridicule?How did I know that your response would be along those lines, I wonder?

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Okay, so what's my position on how the information got into the common ancestor...undirected evolution, of course. The LUCA is believed to have existed long after life originated: long after "random" mutation and natural selection were operating on living entities.

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LUCA could be the same as the human mitochondrial Eve. Even though there were human females before the mitEve, that mito. line is still the common ancestor for all humans. In this context, it is easy to accept LUCA as the first common ancestor, but not the first life. Information due to evolutionary mechanisms would already be present.However, my question is this. Is there a baseline information content for a random sequence of DNA. To be more exact, if we came up with a random open reading frame, with an appropriate promoter, would we expect some kind of activity from the translated protein? Even though this random protein may not have enzymatic or catalytic properties, I would bet a hundred bucks we could find something that it bound to. Perhaps the baseline information content of any DNA sequence is its ability to be transcribed and translated. Perhaps the earliest DNA information was actually a promoter site and the lack of stop codons. Just a thought.

program/data distintion is quite straight forward ....data doesn't perform any operations, program does.I agree though -- any analogy can be useful so long as it
is relevent.

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And yet you responded as if I were wrong!?!?

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On a grammatical point it should read:
'And yet you responded as if I was wrong'unless, of course, the possibility of you being wrong
is zero. What's the matter, can't you write or something ... oh and I responded because you ARE wrong, just didn't want
to get sidetracked -- but couldn't leave it for you to think
people agreed with you.

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Peter: You don't need even distribution (spatially) for the mutations to be random ...

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DNA asks:
Why are you addressing a statement I didn't make?

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DNA wrote:-
In such genomes, because the mutations are not evenly distributed, technically, they are not random.

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Didn't you write that?Everything else you posted is irrelevent because:ANY location on a DNA strand CAN suffer a mutation.
Hotspots don't always suffer mutations.I have a suggestion for you, before you post any more quotations
consider whether they add or subtract from the message you
are giving, and whether they support your position or not.

I think Ooook asked your opinion on the origin or
information in THE common ancestor (i.e. the
first ever 'This is definitely life' cell).So you are avoiding the question ... besides you KNOW
what is being asked so failing to provide an answer
(even if that answer is 'I don't want to say.') is
reprehensible.

Ooooh! - So close, but still not there! I believe we can make it
there with just a little more effort.You said this: And at the big reveal gave me this: I wasn't at all surprised with this response, just disappointed.You keep on urging to use their eyes and read what you say, I
emplore you now to use your brain. Stop the pointless nitpicking
and try and see what everybody is getting at. Use a bit of that
logic that you claim others lack, and your knowledge of molecular
biology to get the gist of my argument.You do have that knowledge don't you? You didn't just sit there
with a pile of biochemistry books and look in the indexes for
'information'?To make it easier for you I'll draw you a little picture. How's
that?DNA/RNA ---------------------------------> DNA/RNA/ProteinSomewhere along the dotted line, your much touted 'information' got into the DNA in order for it to encode for proteins. How do think that happened?

Your question was completely ridiculous: any rational and honest person knows that. You moved from the original topic to an analogy that didn't maintain correspondence to the original: you changed one or more key factors which makes the analogy invalid.In fact, this is typical of you...you use strawmen against me, in just about every exchange between us (then you turn around and call me an asshole). You substitute your much weaker replacements, of your own conjuring, and then attack those substitutes, and in doing so pretend to have suceeded in knocking down my original.So Crashfrog, it's your argument - you have the burden of proof to show that it is legitimate...so go ahead.[This message has been edited by DNAunion, 03-25-2004]

So explain how. What factors? My analogy demonstrates that when people use the word "random", they do so without reference to the spacial location of the event in question. You haven't even come close to defending your interpretation of random, yet. Oh, please.

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Your question was completely ridiculous: any rational and honest person knows that. You moved from the original topic to an analogy that didn't maintain correspondence to the original: you changed one or more key factors which makes the analogy invalid.

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Crashfrog: So explain how.

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Not my job. You offered something ridiculous. You think it’s notdemonstrate that it’s not.

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Crashfrog: You haven't even come close to defending your interpretation of random, yet.

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You can’t read, can you. I have supported my position (I guess because some of the words have more than 4 letters you couldn't understand what was being said).And here’s more.I remembered one of the most anti-Creationist, hard core evolutionists — Richard Dawkins — saying that mutations weren’t technically random in some respects, but had sold off all of my books by him (and many others). So I used Google on Dawkins mutation not random and got this hit. I’m trusting that the person who quoted Dawkins did so legitimately.

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We can now see that the question of whether mutation is really
random is not a trivial question. Its answer depends on what we
understand random to mean. If you take 'random mutation' to mean
that mutations are not influenced by external events, then X-rays
disprove the contention that mutation is random. If you think
'random mutation' implies that all genes are equally likely to
mutate, then hot spots show that mutation is not random. If you
think 'random mutation' implies that at all chromosomal loci the
mutation pressure is zero, then once again mutation is not random.
It is only if you define 'random' as meaning 'no general bias towards
bodily improvement' that mutation is truly random." (Dawkins R.,
"The Blind Watchmaker", Penguin: London, 1991, p307)

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"There is a fifth respect in which mutation might have been non-random. We can imagine (just) a form of mutation that was
systematically biased in the direction of improving the animal's
adaptedness to its life. But although we can imagine it, nobody has
ever come close to suggesting any means by which this bias could come
about. It is only in this fifth respect, the 'mutationist' respect,
that the true, real-life Darwinian insists that mutation is random.
Mutation is not systematically biased in the direction of adaptive
improvement, and no mechanism is known (to put the point mildly) that
could guide mutation in directions that are non-random in this fifth
sense. Mutation is random with respect to adaptive advantage,
although it is non-random in all sorts of other respects. It is
selection, and only selection, that directs evolution in directions
that are non- random with respect to advantage." (Dawkins R., "The
Blind Watchmaker", Penguin: London, 1991, p312)

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As I said, there are reasons to consider mutations not to be random, even when they are not directed by intelligence. And, we shouldn't be getting bogged down in this anyway as the original complaint about my putting "random" in quotes is bogus and refuted.