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Author Topic:   Definition of Species
fiedel 
Suspended Junior Member (Idle past 4641 days)
Posts: 2
Joined: 07-13-2011


Message 346 of 450 (623757)
07-13-2011 6:03 AM


Re: Definition of species
Oh, a signature spammer. Bye guy! --Admin
(1) The lowest taxonomic rank, and the most basic unit or category of biological classification.
(2) An individual belonging to a group of organisms (or the entire group itself) having common characteristics and (usually) are capable of mating with one another.
A species is given a two-part name: the generic name and the specific name (or specific epithet). For example, Allium cepa (commonly known as onion)
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Big_Al35
Member (Idle past 799 days)
Posts: 389
Joined: 06-02-2010


Message 347 of 450 (624489)
07-18-2011 7:01 AM
Reply to: Message 344 by Percy
07-10-2011 6:12 PM


Re: Gene Deletion
Percy writes:
but if you'd like to do that then the thread's open and available
Ok in that case I will continue...
I think I have been right all along in pressing for proper identification of a gene difference. The example we have is MHY16 which is quite a good example as it is functional in chimps but not in humans. One of the reasons that it is not functional in humans is due to a frameshift.
MHY16 is classed as a defective frame-shifted allele in humans. Frame-shift is when DNA across species, which may be very similar, (as in the case of humans and chimps) produces very different genes. ie sequences of DNA which are almost identical will produce different proteins because the start and end points for reading the code are different. Maybe WK or one of the other biologists here could elaborate on this point.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 348 of 450 (624500)
07-18-2011 10:05 AM
Reply to: Message 347 by Big_Al35
07-18-2011 7:01 AM


Frameshifts
I think I have been right all along in pressing for proper identification of a gene difference.
Care to explain why?
Frame-shift is when DNA across species, which may be very similar, (as in the case of humans and chimps) produces very different genes.
There is no need to bring species into this in terms of a definition, frame-shift mutations can produce mutations just as readily trans-generationally. Indeed there are probably many cells within your own body hosting frameshift mutations.
sequences of DNA which are almost identical will produce different proteins because the start and end points for reading the code are different. Maybe WK or one of the other biologists here could elaborate on this point.
When mRNA sequences are translated into protein sequences the correct amino acid for each step of the protein synthesis is determined by a 3 nucleotide long 'codon' after an amino acid has been incorporated the next 'codon' determines the subsequent amino acid in the protein synthesis. The way that a given sequence translates based on a particular start site is called its reading frame. Any stretch of nucleotides has 3 reading frames, but traditionally only 1 is thought to be functional (although some recent research disagrees).
Because of this arrangement insertion or deletion mutations that are not a multiple of 3 can cause frameshifts because all the codons downstream of such a mutation have had their reading frame altered, or shifted, by whatever size the insertion/deletion was. This means that a frameshift mutation can alter every single amino acid coded by the sequence that comes after the codon affected by the mutation.
This makes frameshifts one of the more radical forms of mutation at the level of genes. It is a simple one step change which can render a protein non-functional. It is also a mechanism which there is some evidence to support as a source of the de-novo generation of new genes, as in the Nylonase digesting enzymes (Ohno, 1984) or in a number of human genes (Knowles and McLysaght, 2009).
TTFN,
WK

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Replies to this message:
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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 349 of 450 (624560)
07-18-2011 5:12 PM
Reply to: Message 347 by Big_Al35
07-18-2011 7:01 AM


Re: Gene Deletion
Maybe WK or one of the other biologists here could elaborate on this point.
WK did a wonderful job of describing what a frameshift mutation is. I will only add this illustration:
The result of the frameshift mutation in the human myosin gene was a dysfunctional protein due to the massive difference in amino acid sequence caused by the addition (or deletion) of DNA. The result was a weaker jaw muscle. A weaker jaw muscle requires less bone as an anchor. Less bone needed to anchor the jaw muscle allows for a larger cranium, and hence a larger brain.
As a counterexample, take a look at this gorilla skull. Notice the massive crests necessary for anchoring the large jaw muscles.

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Big_Al35
Member (Idle past 799 days)
Posts: 389
Joined: 06-02-2010


Message 350 of 450 (624635)
07-19-2011 6:15 AM
Reply to: Message 348 by Wounded King
07-18-2011 10:05 AM


Re: Frameshifts
One point about frameshift mutations is that their impact is likely to be very significant and more so than one might expect.
If we take a phrase ie
THE CAT ATE THE RAT END where END represents the stop codon and then introduce a frameshift on this we might get something like
THE CAA TAT ETH ERA TEN D
As you can see the meaning of the sentence is completely lost and the full stop has gone too. Any subsequent sentence could also become gibberish. The few examples of frameshift mutations that I have come across in humans often have terrible consequences eg
Duchenne muscular dystrophy and Tay Sachs. If you know of any beneficial mutations that would be intriguing.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 351 of 450 (624638)
07-19-2011 6:57 AM
Reply to: Message 349 by Taq
07-18-2011 5:12 PM


Re: Gene Deletion
I looked it up and the actual mutation in the human lineage is a 2 base deletion in exon 18 of the gene. This deletion introduces a stop codon about 30 bases further downstream. This results in the protein being truncated from its expected size of 223 kilodaltons down to 76 kilodaltons.
Interestingly the gene is still transcriptionally active in a tissue specific fashion, being expressed in the jaw muscles as it is in other primates.
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 352 of 450 (624640)
07-19-2011 8:03 AM
Reply to: Message 350 by Big_Al35
07-19-2011 6:15 AM


Re: Frameshifts
If you know of any beneficial mutations that would be intriguing.
Do you mean a modern contemporary spontaneous beneficial frameshift mutation in the human population?
TTFN,
WK

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 Message 350 by Big_Al35, posted 07-19-2011 6:15 AM Big_Al35 has replied

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 353 of 450 (624763)
07-19-2011 8:45 PM
Reply to: Message 350 by Big_Al35
07-19-2011 6:15 AM


Re: Frameshifts
The few examples of frameshift mutations that I have come across in humans often have terrible consequences
Except the one that allowed for one of the most important evolutionary changes in the hominid lineage, the MYH frameshift mutation that allowed for the expansion of the brain.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 354 of 450 (624803)
07-20-2011 5:03 AM
Reply to: Message 353 by Taq
07-19-2011 8:45 PM


Re: Frameshifts
Except the one that allowed for one of the most important evolutionary changes in the hominid lineage, the MYH frameshift mutation that allowed for the expansion of the brain.
To be fair that is pretty much speculation. The fact that the mutation's origin coincided with the expansion of the brain, give or take a few million years is far from conclusive as to a causative relationship.
Other researchers have suggested that in fact the mutation occurred much closer to the original chimp-human lineage split (Perry et al, 2005) rather than alongside the appearance of Homo in the fossil record as Stedman et al. (2004) suggested.
McCollum et al (2006) wrote a review bringing forward several lines of evidence calling into question Stedman's hypothesis as to the significance of MYH16. These included the timing of the mutation, the known effects of jaw musculature on constraining brain development and the fact that the majority of brain development occurs well before such muscles are well established and developed to their full force generating potential.
TTFN,
WK

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Big_Al35
Member (Idle past 799 days)
Posts: 389
Joined: 06-02-2010


Message 355 of 450 (625007)
07-21-2011 5:33 AM
Reply to: Message 352 by Wounded King
07-19-2011 8:03 AM


Re: Frameshifts
WK writes:
Do you mean a modern contemporary spontaneous beneficial frameshift mutation in the human population?
Yes, let's focus on humans rather than chimpanzees for the time being. I would be interested in any human to human examples of frameshifted alleles which might generate new traits or features for an individual.
Only from this context can we then move on to presuppose frameshifting across the species.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 356 of 450 (625014)
07-21-2011 7:03 AM
Reply to: Message 355 by Big_Al35
07-21-2011 5:33 AM


Re: Frameshifts
Only from this context can we then move on to presuppose frameshifting across the species.
Why on earth do you think this?
Any other ludicrous and irrelevant stipulations you want to make? Can we only consider macroevolution if the moon is made of green cheese?
Contemporary beneficial mutations of any kind in human populations are incredibly hard to detect. Unlike deleterious mutations with obvious major phenotypes, such as Tay-Sachs, no one is brought into hospital as the result of beneficial mutation.
We can only detect beneficial mutations through exhaustive longitudinal studies over generations and capturing the initial generation of one de novo and then following it would be almost impossible.
There are some plausible already extant candidates however. One example would be the CCR5 delta-32 isoform. This is a frameshifted version of the CCR5 gene which has undergone a 32bp deletion and produces a severely truncated protein. This mutation appears to confer a degree of protection from HIV-1 (Trecarichi et al. 2006). Some researchers have suggested that the prevalence of this mutation is simply consistent with neutral evolution (Sabeti et al., 2005) but a more recent review (Oleksyk et al., 2010) outlines a number of flaws with this position. Either way the origin of this mutation is probably between 1000 to 5000 years ago so whatever selective pressure it was susceptible to it is unlikely to have been HIV-1 infection. Whether it will now be a target of selection due to HIV-1 is an open question which only future transgenerational studies will reveal.
TTFN,
WK

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Big_Al35
Member (Idle past 799 days)
Posts: 389
Joined: 06-02-2010


Message 357 of 450 (625016)
07-21-2011 7:21 AM
Reply to: Message 348 by Wounded King
07-18-2011 10:05 AM


Re: Frameshifts
WK writes:
Any other ludicrous and irrelevant stipulations you want to make? Can we only consider macroevolution if the moon is made of green cheese?
WK writes:
frame-shift mutations can produce mutations just as readily trans-generationally. Indeed there are probably many cells within your own body hosting frameshift mutations.
Aha, so you are also guilty of making wild generalisations without evidence to back up your claims. I'll take your previous comment as bullshit then.

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 Message 348 by Wounded King, posted 07-18-2011 10:05 AM Wounded King has replied

Replies to this message:
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Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 358 of 450 (625028)
07-21-2011 8:01 AM
Reply to: Message 357 by Big_Al35
07-21-2011 7:21 AM


Re: Frameshifts
Hi Big Al,
I think you misunderstand what WK is saying. The "ludicrous and irrelevant stipulation" he refers to is not the possibility of frameshift mutations, but your statement that, "Only from this context [human to human frameshift mutations] can we then move on to presuppose frameshifting across the species." The question is, what does this mean?
WK and I are at opposite ends of the spectrum in interpreting your posts. I believe you do not often understand the details we're discussing and that much of what you say does not make sense. WK believes that what you're saying does make sense, and so he imposes upon your words an interpretation and meaning that I believe is not actually there.
So in your statement about presupposing frameshift mutations, I saw it and thought it fairly resistant to any unambiguous interpretation and probably reflecting more confusion. WK saw it and thought you were making an inappropriate presupposition. In any case, in your quoted passages his latter statement does not contradict his first.
--Percy

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Big_Al35
Member (Idle past 799 days)
Posts: 389
Joined: 06-02-2010


Message 359 of 450 (625029)
07-21-2011 8:05 AM
Reply to: Message 351 by Wounded King
07-19-2011 6:57 AM


Re: Gene Deletion
WK writes:
I looked it up and the actual mutation in the human lineage is a 2 base deletion in exon 18 of the gene. This deletion introduces a stop codon about 30 bases further downstream. This results in the protein being truncated from its expected size of 223 kilodaltons down to 76 kilodaltons.
In this MYH16 mutation, it turns out that this frameshift caused a punctuation mark (aka a stop codon) to just pop up — so the protein is cut off far sooner than it should be! Not too good for any traits relying on that protein.
So far from it actually pushing the stop codon further downstream as we had previously implied it appears that the stop codon appears earlier in the sequence. If you were a software engineer you could think of it as like commented out code.

This message is a reply to:
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Replies to this message:
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Big_Al35
Member (Idle past 799 days)
Posts: 389
Joined: 06-02-2010


Message 360 of 450 (625032)
07-21-2011 8:12 AM
Reply to: Message 358 by Percy
07-21-2011 8:01 AM


Re: Frameshifts
WK and I are at opposite ends of the spectrum in interpreting your posts
One minute WK suggests that frameshifting is likely to be evident even in my own body and the next he says that there is no chance of getting any hard evidence to prove this point.
All I asked for was some examples of this and some evidence. How can this possibly be misinterpreted?

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Replies to this message:
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