Re: Part 1 (of 3): What are major aspects of evolutionary theory?

anon1@xxxxxxx wrote:

>>>the report seems
>>>to say that old idea was wrong, that there's such a drastic difference
>>>between hot and cool spots that to a good approximation the chromosomes
>>>are strictly divided into fixed blocks that act as units during meiosis.
>>
>>Very interesting if so, though it contradicts all sorts of other data.
>
>
> Note that haplotype blocks that are very nearby may take several
> generations before they have even a 50% chance of a cross-over between
> them, thereby separating them. But over long terms (tens of thousands
> of years), they eventually get separated, so what I'm saying above
> refers to such long terms.

I wasn't talking about independent assortment between haplotype blocks.
I was talking about the very existence of haplotype blocks as stable
entities.

> Note that there are just over 3000 million base pairs, which averages
> to more than 100 million per chromosome. So even if there are thousands
> of DNA bases per haplotype block (typically, not universally), that's
> still less than a thousandth of a chromosome length, which is
> virtually an infinitesimal on any regular chromosome map. At the
> centimorgan scale, haplotype blocks of such size don't show up.
> (That's my impression anyway. CMIIM)

That's what I was wondering about.

>>Thanks for the information. I'm a bit dubious about the constancy of
>>these haplotype blocks. How big are they?
>
> I don't remember from browsing the article in _Science_.
> I'm hoping somebody here has that information and can answer.
> (I think I already asked what the statistics of haplotype-block lengths
> are, and nobody answered. So maybe I'll have to re-post my question on
> the other newsgroup, the more professional one, which spends most of
> its time arguing over Hamilton's equation, you know which one, right?)
>
>
>>><http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-L/linkage_group.html>
>>> A group of gene loci known to be linked; a chromosome. There are as
>>> many linkage groups as there are homologous pairs of chromosomes.
>>
>>This definition is wrong. A chromosome would have to be very small to
>>form a single linkage group under most recombination rates. Or have a
>>special mechanism to prevent recombination.
>
> You're mixing up two definitions, the linkage itself, which means
> Mendel's rules for those two specific loci are violated enough to
> directly measure the linkage, and the "linkage group", which is the
> transitive closure of all chains of linkages. It's like the difference
> between a micro-species (part of a "ring species" whereby each
> individual can mate with any other of opposite sex), and the entire
> "ring species" as a whole, where not all pairs of opposite-sex
> individuals can pairwise mate, but there's a chain of such links from
> any individual to any other individual. East-Mongolia and West-Mongolia
> birds can't mate with each other, but East-Mongolia can mate with
> East-China which in turn can mate with Tibet which in turn can mate
> with West-China which in turn can mate with West-Mongolia, or something
> like that. So among loci A B C D E, A may be linked with B and C, B
> with C, C with D and E, D with E, so all five are a single "linkage
> group". The entire chromosome is a single linkage group, by such a
> daisy chain of A-link-B-link-C-..., assuming markers are known
> sufficiently close each to the next.

That's not the way it's generally used in my experience.

>
>>>Due to the ambiguity of definition, and the fact that the centroid of
>>>the various definitions simply defines linkage group as the contents of
>>>a chromosome,
>>
>>No, that's not the centroid. The centroid would refer to non-independent
>>assortment.
>
> Huh?? By "centroid" of those conflicting definitions, I merely mean a
> semi-concensus, pick and choose the best of each definition to try to
> guess what the "correct" definition would be, a middle-of-road
> political position, not an extremist.

Right. That's what I mean too. I don't think your semi-consensus is the
correct semi-consensus based on the definitions you have given.

>>>where there are
>>>several different such blocks on each single chromosome.
>>
>>Can you define "several" here? How long are these blocks?
>
>
> I don't remember from the article. Maybe somebody else here knows.
>
>
>>If they're so big as to have only "several" per chromosome,
>
>
> I didn't say *only* several. I said merely *several*, which is most
> likely an understatement. (I must be turning into a Brit!)
>
>
>>then chromosomal mapping by linkage would be impossible, and as this
>>has been done with humans as well as other species, I'm going to
>>suppose that there are lots and lots of blocks per chromosome, so they
>>don't show up at all at the scale of linkage maps.
>
>
> Correct, they're very large by kindergarden arithmetic (longer than a
> hundred bases, maybe longer than that utterly impossible "thousand"),
> but very very small by whole-chromosome-length standards. But I really
> don't remember how long they are. Maybe they really do affect
> linkage-maps, for example where two different genes seem to be at
> exactly the same "locus", which is impossible on first thought, but a
> very large haplotype block would nicely explain that occasional anomaly.
> (I do actually seem to recall seeing in _Science_ some genome of
> something portrayed as just a linkage map, with two genes indicated at
> exactly the same spot on the map, not once but several different such
> cases. But I might be mis-remembering.)
>
>
> By the way, in the midst of just starting to compose this reply, I did
> a Google search about the human genome, to find out the total number of
> DNA bases (which I quoted above, just over 3 billion, actually just
> over 3.1 billion), and saw something somewhere that said there are 30
> thousand genes, of which only half have known function. So I got to
> thinking: Are there really 30 thousand genes, or only 30 thousand open
> reading frames, which aer *presumed* to all be genes, but for all we
> know half of them are suppressed, inactive, don't actually generate
> either RNA or polypeptides. But I wasn't sure I knew the correct
> definition of ORF so I did another Google search, and found rather
> conflicting definitions. Which of these (grouped by synonyms, each
> group contradicts the others) is the correct ORF definition?
>
> <http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-O/open_reading_frame.html>
> A section of a sequenced piece of DNA that begins with an initiation
> (methionine ATG) codon and ends with a nonsense codon. ORFs all have
> the potential to encode a protein or polypeptide, however many may not
> actually do so.
> <http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/O/O.html>
> DNA sequence beginning with ATG and read in triplets until it
> ends with a STOP codon. An ORF is potentially able to encode a
> polypeptide.
> <http://66.102.7.104/search?q=cache:IqPKpi5TztwJ:manatee.sourceforge.net/pdf/overview.pdf+open+reading+frame&hl=en&ie=UTF-8>
> o Telling the difference between random ORFs and
> genes is the goal in the gene finding process.
> (That's the definition I thought was correct, but see the others:)
>
> <http://www.medterms.com/script/main/art.asp?articlekey=4644>
> Open reading frame: A long sequence of DNA that has no stop codon (no
> signal to stop reading) and therefore may encode part or all of a
> protein.
> <http://opbs.okstate.edu/~melcher/MG/MGW2/MG241.html>
> Regions of nucleotide sequences devoid of termination
> codons in one frame of reading are designated "open reading
> frames".
>
> <http://66.102.7.104/search?q=cache:l1xHsaVtaNIJ:hal.weihenstephan.de/genglos/asp/genreq.asp%3Fnr%3D292+open+reading+frame&hl=en&ie=UTF-8>
> A sequence of DNA following an initiation codon that does not contain
> a stop codon. Detection of an open reading frame in DNA implies the
> presence of a gene that codes for a protein.
>
> <http://www.iscid.org/encyclopedia/Open_Reading_Frame>
> A reading frame, in biology, consists of three-nucleotide codon sets
> in either DNA or RNA that are contiguous and non-overlapping. An open
> reading frame (ORF) is a similar sequence that can be translated into
> a protein or a polypeptide.
> In any open reading frame, the start-code sequence or initiation codon
> that begins the protein is methionine ATG, and then stop-code sequence
> or termination codon ends it. The stop sequence is coded by what is
> termed a nonsense codon, or a codon that does not have an RNA match.
> There are only three nonsense codons: amber(UAG) ochre(UAA) and opal
> (UGA). As you can see, each one contains a "U" nucleotide, not normal
> to DNA.
> (That last one is bonkers!! Who wrote it, Archimedes Plutonium??)

It's convoluted and contains much unnecessary information, but it's
really the same as all the others, which match each other. Some forget
to mention the initiation codon, and that's the only difference I can
see. But the way the number of genes is estimated is more complicated
than this. Gene-estimation programs are used to identify genes, introns,
exons, and such, and they rely on a large set of clues. I've never
looked at this in detail, but references can be found on the UCSC genome
browser at least for the gene-finding programs they have used.

> I also found currently-online Web pages which disagree about number of
> human genes. What I read so-far in _Science_ over the past five years
> was that the person who guessed 30K won the bet, because the number was
> actually about 25-30K, but then the number went down lower to maybe
> only 10-20K, but then the number came back up to 30K again. What's the
> latest best-estimate of ORFs (any sequence starting with ATG and being
> of sufficient length before the next stop codon, including both actual
> coding genes and pseudo-genes), and number of only the actual coding
> genes, as two separate questions?

I don't know.

> <http://www.thedoctorwillseeyounow.com/articles/other/genome_4/index.shtml>
> It is believed that
> the human genome has between 50,000 and 100,000 genes.
> (Somebody needs to update their Web site!)
> It is estimated that the sequence of the human genome should be
> completely mapped by approximately the year 2005.
> (Yeah!)

Ah, internet paleontology, or vestiges of the natural history of web
creation.

> <http://www.infoaging.org/b-human-12-glossary.html>
> The human genome is estimated to contain
> about 30-40,000 genes,
> <http://www.schoolscience.co.uk/content/4/biology/abpi/genome/genome3.html>
> With between 30 000 and 40 000 genes,
> <http://www.ornl.gov/sci/techresources/Human_Genome/project/info.shtml>
> The human genome is estimated to contain 20,000-25,000 genes.
> <http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/HGP.html>
> 1. The number of genes turned out to be much smaller than once predicted.
> The two groups came up with slightly different estimates of the number
> of protein-encoding genes, but both in the range of 30 to 38 thousand:
> * and a third of the 100,000 genes that many had predicted would be
> found.
> * (By the end of 2004, the number had been reduced to some
> 20,000-25,000.)

.

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