I just wonder why you're telling me all this.
Because I'm a fundamentalist and these are as basic as it gets. You wanted to make a point about the difference between single nucleotide/base substitutions and indels, well here is where it matters.
AFAIK a silent mutation is one that doesn't change the amino acid at all. A mutation that produces an amino acid that works just as well is called neutral.
Most mutations are neutral because most of them are not in an amino acid sequence. Occasionally one can occur in an amino acid sequence without effect and thus they are silent or neutral.
You mean the intron is not removed, because the splice site is mucked up.
The effect is deleterious, that is the point.
But you were talking about substitutions, not indels. And I know what indels and frame shifts are...
Then why the confusion over indels and single base/nucleotide substitutions. If you knew all along then why derail the discussion by playing semantics with them?
As far as I'm aware, polyQ diseases like fragile X and Huntington's have nothing to do with frame shifts. Look, you yourself mention what causes Huntington's: CAG repeat expansion is the insertion of threes of bases! The problem is that an extra-long string of glutamines distorts the protein's structure.
They have everything to do with idels, that is what I am talking about. What is getting lost in these discussions is the major insertions and deletions that are supposed to be responsible for human evolution from the apes and the deleterious effects that would have resulted. From the article I quoted from:
Fragile X Syndrome
Several disorders in humans are caused by the inheritance of genes that have undergone insertions of a string of 3 or 4 nucleotides repeated over and over. A locus on the human X chromosome contains such a stretch of nucleotides in which the triplet CGG is repeated (CGGCGGCGGCGG, etc.). The number of CGGs may be as few as 5 or as many as 50 without causing a harmful phenotype (these repeated nucleotides are in a noncoding region of the gene). Even 100 repeats usually cause no harm. However, these longer repeats have a tendency to grow longer still from one generation to the next (to as many as 4000 repeats).
This causes a constriction in the X chromosome, which makes it quite fragile. Males who inherit such a chromosome (only from their mothers, of course) show a number of harmful phenotypic effects including mental retardation. Females who inherit a fragile X (also from their mothers; males with the syndrome seldom become fathers) are only mildly affected.
This image shows the pattern of inheritance of the fragile X syndrome in one family. The number of times that the trinucleotide CGG is repeated is given under the symbols. The gene is on the X chromosome, so women (circles) have two copies of it; men (squares) have only one. People with a gene containing 8090 repeats are normal (light red), but this gene is unstable, and the number of repeats can increase into the hundreds in their offspring. Males who inherit such an enlarged gene suffer from the syndrome (solid red squares). (Data from C. T. Caskey, et al.).
Huntington's Disease
In this disorder, the repeated trinucleotide is CAG, which adds a string of glutamines (Gln) to the encoded protein (called huntingtin). The abnormal protein increases the level of the p53 protein in brain cells causing their death by apoptosis
.
Notice the effects of Huntington's disease on brain cells and note, the only effects on brain related genes are deleterious or neutral. Show me the adaptive or beneficial ones and you will be the first.
And again, they have nothing to do with frame shifts
or the protein itself (I wrote part of an essay on myotonic dystrophies, so I happen to know what mutations cause them...) In DM type 1, CTG expansion happens in the
3' untranslated region of the
DMPK gene. In DM type 2, the expansion is in an
intron of a zinc finger protein gene. These three reviews discuss myotonic dystrophies:
Faustino NA, Cooper TA (2003) Pre-mRNA splicing and human disease.
Genes & Dev. 17:419-437
Ranum LPW, Day JW (2004) Myotonic dystrophy: RNA pathogenesis comes into focus.
Am. J. Hum. Genet. 74(5):793-804
Ranum LPW, Cooper TA (2006) RNA-mediated neuromuscular disorders.
Annu. Rev. Neurosci. 29:259-277
Care to show me any evidence of that "reality"?
I said the most likely effect from in indel was a frameshift, there are exceptions. Again from the article cited, quoted and linked:
Indels of three nucleotides or multiples of three may be less serious because they preserve the reading frame (see Patient E above).
However, a number of inherited human disorders are caused by the insertion of many copies of the same triplet of nucleotides. Huntington's disease and the fragile X syndrome are examples of such trinucleotide repeat diseases.
Not Piltdown Man again, please.
Piltdown is a prime example of the deception evolutionists are famous for. I ask you one time and one time only. What is the percentage of difference between the DNA of humans and chimpanzees? Do include the indels thought to be responsible for our divergence from apes and continue reading to the end before you answer.
What other false evidence are you referring to? A measure of similarity that has to be adjusted by a few per cent is hardly "false". And hardly comparable to deliberate fraud...
Keep thinking and remember we are not talking about a few unimportant percentage points but millions of base pairs.
Who said it was supposed to indicate the whole difference? In that paper, it was explicitly stated what the 98% measured, so anyone misinterprets it at their own risk. Presumably, the studies they cited also stated what they measured, otherwise they wouldn't be cited under the "substitutions in orthologous positions" heading.
From Nature's Web Focus article on the Intitial Sequence of the Chimpanzee Genome:
What makes us human? We share more than 98% of our DNA and almost all of our genes with our closest living relative, the chimpanzee. Comparing the genetic code of humans and chimps will allow the study of not only our similarities, but also the minute differences that set us apart.
Chimp Genome
From the article they are announcing:
Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements...
...On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 4045 Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total ~90 Mb. This difference corresponds to ~3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions; this confirms and extends several recent studies. Of course, the number of indel events is far fewer than the number of substitution events (approx5 million compared with ~35 million, respectively).
Initial sequence of the chimpanzee genome and comparison with the human genome
Now I ask you, which statement is true and which is false because the first is saying 98% and the other is saying close to 95%. What is being compared is the DNA, nothing fancy in the first statement indicates anything else. The two cannot be true, one is true and one is false. Choose or explain.
For the phenotypic differences, how exactly? If anything, more genetic divergence makes it easier.
The genetic differences are considerable but mainstream science is not being forthcoming with the actual differences. They are too obsessed with homology arguments to be honest about them.
96% or whatever is still pretty damn close for completely unrelated organisms.
What is represented by that 4% though? That is what is important and is it 96% or is it 99%? Choose or explain
Yes, and with better knowledge of both genomes, we know that there are other factors at work. Duplications, gene losses, structural differences, what have you. How that argues against our common ancestry escapes me.
Because every step in the evolutionary scenario has to be accounted for because everytime an amino acid sequence is changed the effects, the vast majority of the time, are deleterious. When they affect the brain they are always deleterious which is why brain related genes are so often named for the diseases and disorders resulting from mutations.
Point being? Growing =/= too high to be believed. And every time you want to pull out "highly conserved genes", remember the last half-million years of
OdsH, please.
It don't work that way, it had to have happened 2 mya just like most of the evolutionary giant leaps you are being brain washed into believing actually happened.
Selective pressures change.
With limits, see my signature.
Right. You have certain central points you keep going back to after being corrected on them numerous times (like this whole sudden brain leap thing of yours). I guess we've found a reason why nobody ever concedes a point to you.
Probably why they keep using the same outdated and disproven homology arguments.
That depends on the adaptation. Haemoglobin adapts to height (or malaria) via amino acid substitutions, stickleback pelves grow or shrink due to changes to regulatory sequences... I could probably find examples of just about every possible kind of mutation involved in some adaptation if I took the time to look.
You will have to but not to prove any points to me. There is no way of accounting for adaptations without these kinds of changes but you must forever bear in mind there are limits.
EDIT: how could I forget about a very famous adaptation caused by a frame shift? Nylonase FTW!
Something times 10[sup]-8[/sup] per site per generation seems a reasonable ballpark to me.
I'll venture a guess that no matter how much material on human evolution we have, many other cases are better understood.
Would be nice to quote specific examples.
Calling you out on a mistake isn't automatically fallacious.
Speaking of mistakes and quoting from the Scientific American you tell me if this statement is true or false:
Six years ago I jumped at an opportunity to join the international team that was identifying the sequence of DNA bases, or 'letters,' in the genome of the common chimpanzee (Pan troglodytes). As a biostatistician with a long standing interest in human origins, I was eager to line up the human DNA sequence next to that of our closest living relative and take stock. A humbling truth emerged: our DNA blueprints are nearly 99 percent idntical to theirs. That is, of the three billion letters that make up the human genome, only 15 million of them - less then 1% - have changed in the six million years or so since the human and chimp lineages diverged." (Scientific American May 2009)
Now, look again at the International Chimpanzee Consortium's actual comparison and tell me how you come to 99%. Bear in mind she is using terms like 'genome' which indicates whole genome comparisons and tell me how she could make such a fundamental mistake.
You have to choose or explain, how can the comparison be 99% and 96% at the same time. Time lied about this as did Nature Focus and so did she, that is my explanation, what is yours?