42 wrote...
Oh great, we've mapped the whole human genome, we know everything then, we can go home now.
That'd sting if I said anything along those lines. as it is though you seem fairly prominent in the straw man department.
As it stands, I predict this is going to be a fun post.
The efforts to identify and analyze all of our 20.000 genes (and sequencing the multiple variations of each one of these 20.000 genes) achieved great results so far, but is far, far, far from over.
I don't dispute that at all.
Even the most famous project to code our DNA (HGP) didn't sequence everything after 20 years of effort as 8~10% of our DNA remains untouched (heterochromatic DNA), let alone the fact that these 20.000 genes are only the protein-coding ones, which accounts for only a ridiculous small portion of human DNA, 2%.
Actually it's a little less than that. But whatever. The actual fact of the matter that you seem to be skipping over is that the Human Genome Project DID successfully map out the entire human genome. The problem is, we don't know what the vast majority of it DOES. Francis Collins, who was the head of the project, did use the end result, however, to point out that evolution is pretty much proven by the DNA alone. So it's not like they didn't find a substantial bit of information in these projects. Not that I'm saying you SAID that, simply that it seems you're implying we know next to nothing about genetics, which is hardly the case at all.
The rest 98% are Noncoding DNA, which does have a function as the ENCODE project have shown, we just don't know precisely which yet, so yeah, I would say our current understanding of human DNA is very far from clear.
Not only does the other OVER 98% have a function, but we know what many of those functions are. Here are some:
Protection of the Genome
Noncoding DNA separate genes from each other with long gaps, so mutation in one gene or part of a chromosome, for example deletion or insertion, does not have the "frameshift mutation" on the whole chromosome. When genome complexity is relatively high, like in the case of human genome, not only different genes, but also inside one gene there are gaps of introns to protect the entire coding segment to minimise the changes caused by mutation.
Genetic switches
Some noncoding DNA sequences are genetic "switches" that regulate when and where genes are expressed.
Regulation of gene expression
Main article: Regulation of gene expression
Some noncoding DNA sequences determine the expression levels of various genes.
Transcription factors
Some noncoding DNA sequences determine where transcription factors attach. A transcription factor is a protein that binds to specific non-coding DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA. Transcription factors act at very different locations on the genomes of different people.
Operators
An operator is a segment of DNA to which a repressor binds. A repressor is a DNA-binding protein that regulates the expression of one or more genes by binding to the operator and blocking the attachment of RNA polymerase to the promoter, thus preventing transcription of the genes. This blocking of expression is called repression.
Enhancers
An enhancer is a short region of DNA that can be bound with proteins (trans-acting factors), much like a set of transcription factors, to enhance transcription levels of genes in a gene cluster.
Promoters
A promoter is a region of DNA that facilitates transcription of a particular gene. Promoters are typically located near the genes they regulate.
Insulators
A genetic insulator is a boundary element that plays two distinct roles in gene expression, either as an enhancer-blocking code, or rarely as a barrier against condensed chromatin. An insulator in a DNA sequence is comparable to a linguistic word divider such as a comma (,) in a sentence, because the insulator indicates where an enhanced or repressed sequence ends.
it's even known WHAT a lot of these bits of noncoding DNA are.
For instance:
Noncoding functional RNA
Noncoding RNAs are functional RNA molecules that are not translated into protein. Examples of noncoding RNA include ribosomal RNA, transfer RNA, Piwi-interacting RNA and microRNA.
MicroRNAs are predicted to control the translational activity of approximately 30% of all protein-coding genes in mammals and may be vital components in the progression or treatment of various diseases including cancer, cardiovascular disease, and the immune system response to infection.
Cis- and Trans-regulatory elements
Cis-regulatory elements are sequences that control the transcription of a nearby gene. Cis-elements may be located in 5' or 3' untranslated regions or within introns. Trans-regulatory elements control the transcription of a distant gene.
Promoters facilitate the transcription of a particular gene and are typically upstream of the coding region. Enhancer sequences may also exert very distant effects on the transcription levels of genes.
Introns
Introns are non-coding sections of a gene, transcribed into the precursor mRNA sequence, but ultimately removed by RNA splicing during the processing to mature messenger RNA. Many introns appear to be mobile genetic elements.
Studies of group I introns from Tetrahymena protozoans indicate that some introns appear to be selfish genetic elements, neutral to the host because they remove themselves from flanking exons during RNA processing and do not produce an expression bias between alleles with and without the intron. Some introns appear to have significant biological function, possibly through ribozyme functionality that may regulate tRNA and rRNA activity as well as protein-coding gene expression, evident in hosts that have become dependent on such introns over long periods of time; for example, the trnL-intron is found in all green plants and appears to have been vertically inherited for several billions of years, including more than a billion years within chloroplasts and an additional 2–3 billion years prior in the cyanobacterial ancestors of chloroplasts.
Pseudogenes
Pseudogenes are DNA sequences, related to known genes, that have lost their protein-coding ability or are otherwise no longer expressed in the cell. Pseudogenes arise from retrotransposition or genomic duplication of functional genes, and become "genomic fossils" that are nonfunctional due to mutations that prevent the transcription of the gene, such as within the gene promoter region, or fatally alter the translation of the gene, such as premature stop codons or frameshifts. Pseudogenes resulting from the retrotransposition of an RNA intermediate are known as processed pseudogenes; pseudogenes that arise from the genomic remains of duplicated genes or residues of inactivated genes are nonprocessed pseudogenes.
While Dollo's Law suggests that the loss of function in pseudogenes is likely permanent, silenced genes may actually retain function for several million years and can be "reactivated" into protein-coding sequences and a substantial number of pseudogenes are actively transcribed. Because pseudogenes are presumed to change without evolutionary constraint, they can serve as a useful model of the type and frequencies of various spontaneous genetic mutations.
Repeat sequences, transposons and viral elements
Transposons and retrotransposons are mobile genetic elements. Retrotransposon repeated sequences, which include long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), account for a large proportion of the genomic sequences in many species. Alu sequences, classified as a short interspersed nuclear element, are the most abundant mobile elements in the human genome. Some examples have been found of SINEs exerting transcriptional control of some protein-encoding genes.
Endogenous retrovirus sequences are the product of reverse transcription of retrovirus genomes into the genomes of germ cells. Mutation within these retro-transcribed sequences can inactivate the viral genome.
Over 8% of the human genome is made up of (mostly decayed) endogenous retrovirus sequences, as part of the over 42% fraction that is recognizably derived of retrotransposons, while another 3% can be identified to be the remains of DNA transposons. Much of the remaining half of the genome that is currently without an explained origin is expected to have found its origin in transposable elements that were active so long ago (> 200 million years) that random mutations have rendered them unrecognizable.[19] Genome size variation in at least two kinds of plants is mostly the result of retrotransposon sequences.
Telomeres
Telomeres are regions of repetitive DNA at the end of a chromosome, which provide protection from chromosomal deterioration during DNA replication.
There are other encoding projects which mapped areas which other projects failed to map precisely, but most of these projects map our DNA under their own specific purposes, therefore only accounting the information substantial to that purpose and no definitive concise list of all genes, all of its variations and all of its effects and functions exist. To even start forming such table of information, interdisciplinary contributions would be necessary, mainly from molecular biology which is also a relatively recent field. The sole use of our current understanding of genetics on racial and anthropological studies are not enough to form these biological distinctions. Given this lack of substantial data, we can only make conjectures on genetic studies but not really logical conclusions.
All of this is available after the most cursory of google searches, but sure, what do we REALLY know about genetics, right? The fact of the matter is, the knowledge the scientific community has about genetics is about as 'blurry' as their knowledge about...anything.
Your geneticists.
The mainstream view of geneticists. Not mine, not yours, out of all geneticists, the mainstream view is, "No biological basis for human races."
The efforts to discard the concept of race inside the field of human genetics started in the 70s mostly by Lewontin's studies. He used mathematical models to organize and compute the “genetic markers” of race and he concluded that race doesn't exist in humans given the absurd variation he found inside populations rather than between. From his studies and the social rejection of the definition of race as bigotry, many scientists in the 90s and 2000s and recently 2010s followed his conclusions by affirming that race doesn't exist.
Well I find this to be a red herring at best as I never even brought up Lewontin, but sure, if you wanna go there, I don't mind explaining why you're wrong here either.
I'll go ahead and go with Dawkins' um...'refutation' so to speak since you say at the end of your post you're on Dawkins' side here. In The Ancestor's Tale he quotes Lewontin speaking on human diversity. Here's Lewontin:
"Human racial classification is of no social value and is positively destructive of human and social relations.Since such racial classification is now seen to be of virtually no taxonomic or genetic significance either, no justification can be offered for its continuance."
Now, Dawkins agrees with the first part of Lewontin's statement. The problem here is that it is not a scientific opinion, it's just an opinion. While Dawkins goes on to agree with Lewontin's first statement
"We can all happily agree that human racial classification is of no social value and is positively destructive of human and social relations. That is one reason why I object to ticking boxes in forms and why I object to positive discrimination in job selection."
The second part of Lewontin's quote...is true. It was true before Lewontin and it's been true decades after. There's a paper: by Kaplan, Jonathan Michael and Rasmus Gronfeldt Winther. "Prisoners of Abstraction? The Theory and Measure of Genetic Variation, and the Very Concept of 'Race.'" 3-5, 8-11. 20 Jul 2012. Biological Theory. Print. I don't have a link, but it's free on school paper databases for you to look up for yourself, demonstrating such. And it's only months old. Fuck, this has been pointed out since DARWIN'S time, prior to us knowing pretty much anything ABOUT genetics aside form basic Mendellian theory. A simple look through "The Descent of Man" shows Darwin pointing out how pointless the whole process of trying to distinguish races seems.
"But the most weighty argument against treating the races of man as distinct species. They graduate into each other independently in many cases, as far as we can judge, of their having intercrossed. Man has been studied more carefully than any other organic being, yet there is the greatest possible diversity amongst capable judges whether he should be classified as a single species, or race, or as two(Virey), as three(Jacquinot), as four(Kant), five(Elumenbach), six(Buffon), seven(Hunter), eight(Aggasiz), eleven(Pickering), fifteen(Boy st. Vincent), sixteen(Desmoulin), twenty two(Morton), sixty(Crawford), or as sixty three according to Burke. this diversity of judgement does not prove that the races ought not be ranked as species, but it shows that they graduate into each other, and it is hardly possible to discover distinctive characters between them." Pages 137-138.
The problem with making a distinction of race, is that when one defines 'race' they are almost always being subjective and arbitrary. Which makes the taxon ranking totally useless on a scientific level.
[uote]But to say “geneticists today agree” with it is going too far. Anthony Edwards - another geneticist fondle of mathematics and molecular biology - was severely critical of Lewontin's Studies and the Fixation Index models in his “
Human Genetic Diversity: The Lewontin's Fallacy”. Risch and Dawkins also point out that Lewinton's conclusions are flawed. And believe me, these three also have a considerable range of followers inside the academic circles, and some believe that the rejection of race in genetics is being politically motivated. Actually, even Edward himself points out that Lewontin's studies were politically motivated, trying to use science as grounds for social equality, which imply in some serious bias on the judgment and presentation of data.[/quote]
The problem here is that the geneticists don't dispute the data being true, they simply dispute Lewontin's research methods, as he showed that he had a clear bias in their outcome. That, however, has nothing to do with the century and a half knowledge we've gained in evolutionary biology and genetics itself, establishing that the SECOND part of Lewontin's quote, is true.
Following these objections a discussion started on the academic circles, mainly from 2004 and onwards, which the papers you showed are from (except Seymour's). And from what I have seen, is still running.
And no evidence to support the racial distinction has been put forth yet. You'd think we'd hang up the argument by now.
This discussion is very heated as not only genetics but many other fields depend on these observations, like forensics, anthropology and sociology, and they're obviously giving their own insights on the issue. Trying to define race by genetics alone already starts to be a problem given this interdisciplinary objection.
It's only heated because it's politically controversial. All the evidence is on one side.
The last substantial comment I saw was from Joseph Graves, which says that both Edward and Lewontin were right, but to me this is just downplaying the bias on Lewontin's studies and trying to find a common ground for both sides, which in turn, doesn't answer anything in regard to the concept of race.
Because they were right. Lewontin was politically motivated, which was rightfully pointed out, but his data was correct. That's the point.
What? Are you serious? You highlight Eddie Hoover paper? Its the most blatantly political, informal and the least scientific of them by far. He goes as far as using vague and emotional expressions as “mother nature” and commits some serious mistakes in regard to genetics. For example, in the second page he goes on to say:
Well let's hope you have a scientific reason to say it's the least scientific...
“In order for race-based research to have any scientific basis, each individually defined or self-declared race would have to have a 100% pure and homogenous gene pool.”
No, it doesn't. By these standards subspecies wouldn't exist even in animals. This is ridiculous, even the most pure of the dog breed doesn't have a completely pure and homogenous gene pool, to require such level of homogenization is just childish.
Then you don't understand what's being referenced. Go back to my first post where I explained derived characteristics. That's what is used for every single taxon ranking. Subspecies is currently the lowest we can go as far as derived characteristics go. Anything below that WOULD require 100% homogonous gene pools. And yes, dog breeds exist, but breeds aren't races, and are certainly far more different than humans are to each other. Why? You should read up on what's known as "The Leap Frog Effect".
People who would be classified as a specific race often lack, due to the diversity of all humans individually, a 'racial characteristic' that is supposed to define them as such. So without that 100% homogeneity, we have nothing to base races on.
I guess you really didn't have a scientific reason. Oh well.
From all these five papers you showed, I would highlight without doubt the American Journal of Human Genetics, much more impartial and informative on the issue.
The other four fail to make a deep analysis on the subject, they circle around the critic of disease markers and protein processors, downplaying the obvious distinctions as “superficial” and ignoring much of the findings on it. Even the American Journal of Human Genetics appeals to the same fallacy by downplaying the discussion on vitamin D synthesis with only one reference and moving forward without showing the other recent papers which point otherwise (like the studies on 1,25-dihydroxycholecalciferol), while the other assertions would generally show a considerable number of references.
Hmmm, wasn't it you who said "“Why 100? One is enough if they're right.”? It's funny how you offer little in the way of refutation on most of the points in the papers, and then vaguely appeal to "other studies" about one very specific point without referencing them, and then pretty much brush off the whole thing as being not enough.
Also, the tone of all papers center around on how to treat race in science, make few allusions to some findings and moving forward the rejection of the race concept and how to use the term race in researches. It's more methodological and political than really a scientific clarification of the facts. This is very clear in Mildred Cho's paper when she goes on to say:
“Scientists and clinicians do not intend to imply hierarchy when they use racial classifications, but it is naive to think that hierarchy can be surgically removed from the concept of race. Hierarchy was an integral part of the concept as originally defined.”
She is basically saying that there is no way to remove the social bigotry from the concept of race inside science, when actually the institution of science is by definition the exclusion of partial and informal directives in the concepts used to discourse and the use of language in its most pure form, not in the historical meaning or context.
So because they move on to explain the political ramifications of the research that denies a biological basis for race, they're not really providing any scientific clarification.
Of course outsiders can misunderstand scientific dissertation and perverse its findings to draw a scenery of oppression, science was used as base for bigotry in the past, but what others do with data should not hamper the search for data itself. If we were to follow her standards, we should also ban the use of gender in scientific methodology, as “it is naive to think that hierarchy can be surgically removed from the concept of gender”.
Yet you don't see scientists arguing over the veracity of gender being biological. Probably because there's an entire chromosomal difference.
On this issue, I still side with Dawkins. I'm still on the opinion that race does exist biologically, the very fact that there is something distinct between one group and the other and something similar inside the same group and distinct from other group point out that something is distinct between groups. The phenotypical differences are not simply a tan or an irregular shape, there is a whole mechanism to create these characteristics, these mechanisms are unique in function therefore it has different results and side-effects between each other, that goes further than simply color or shape. As the results are distinct the mechanism is obviously distinct. It is a biological distinction, they're not the same biologically (if they were, the result would be the same). I recognize this biological distinction but they're not sufficient to imply in any kind of social hierarchy, they are mostly only this, different.
"We can all happily agree that human racial classification is of no social value and is positively destructive of social and human relations. That is one reason why I object to box ticking in forms and why I object to positive discrimination in job selection. But that doesn't mean that race is of “virtually no genetic or taxonomic significance”. This is Edward's point and he reasons as follows. However small the racial partition of the total variation may be if such racial characteristics as there are correlated with other racial characteristics, they are by definition informative and therefore of taxonomic significance."--The Ancestor's Tale: A Pilgrimage to the Dawn of Evolution. Richard Dawkins, Page 407.
This discard of race in genetics is pretty much against the norms of methodological science in which it should account every variance, regardless how negligible it can be.
It's weird how you side with Dawkins and quote the Ancestor's tale, when, within that book, he really only offers two arguments.
The first is inter observer consensus. this is based on the common person's assumptions of human race being a real construct, and the pre conceptualizations of people that they have when you bring up a person's nationality or geographic birthplace. In other words...it's based on stereotypes.
*clap clap* for Dawkins on that one.
in yet if you were to find yourself in the Andaman Islands or Papua New Guinea,and you had no idea where you were, and you just looked at everyone around you, you'd swear you're in africa. And if asked how these people genetically cluster the average person would say, "Well they look African, so they must cluster with africans." when in reality they either fall into their own cluster, or even clusters of people considered to be 'asian or oriental'. See the following papers for this:
Mountain, Joanna and Luigi Luca Cavalli-Sforza. "Multilocus Genotypes, a Tree of Individuals, and Human Evolutionary History." 01 Jan 1997. American Journal of Human Genetics (61). Print.
Thangaraj, Kumarasamy et al. "Genetic Affinities of the Andaman Islanders, a Vanishing Human Population." 26 Nov 2002. Current Biology (in press). Print.
Cordaux, Richard and Mark Stoneking. "South Asia, the Andamanese, and the Genetic Evidence for an 'Early' Human Dispersal Out of Africa." 01 Jan 2003. American Journal of Human Genetics (72). Print.
Endicott, Phillip et al. "The Genetic Origins of the Andaman Islanders." 01 Jan 2003. American Journal of Human Genetics (72). Print.
Kashyap, V.K. et al. "Molecular Relatedness of the Aboriginal Groups of Andaman and Nicobar Islands with Similar Ethnic Populations." 01 Jan 2003. International Journal of Human Genetics (3). Print.
Serre, David and Svante Paabo. "Evidence for Gradients of Human Genetic Diversity Within and Among Continents." 14 Jun 2004. 1682, 1683. Genome Research (14). Print.
-Hill, Catherine et al. "Phylogeography and Ethnogenesis of Aboriginal Southeast Asians." 18 Sep 2006. 17. Molecular Biology and Evolution (in press). Print.
Kayser, Manfred et al. "Melanesian and Asian Origins of Polynesians: mtDNA and Y Chromosome Gradients Across the Pacific." 21 Aug 2006. Molecular Biology and Evolution (23). Print.
And Xu, Shuhua et al. "Genetic Dating Indicates that the Asian-Papuan Admixture Through Eastern Indonesia Corresponds to the Austronesian Expansion." 03 Feb 2012. Proceedings of the National Academy of Sciences (early edition). Print.
Dawkins also goes on in The Ancestor's Tale to say that the classification of race is often subjective, arbitrary, ad bureaucratic. in fact, he feels we're so well meshed together, you could wipe out all but one 'race' of humans and most of human diversity would still be preserved.
"If all humans were wiped out except for one local race, the great majority of genetic variation within the human species would be preserved. This is not intuitively obvious and may be quite surprising to some people. If racial statements were as informative as most Victorians, for example, used to think, you would surely need to preserve a good spread of all the different races in order to preserve most of the variation within the human species. Yet this is not the case." (The Ancestor's Tale, Page 336.)
The only other argument Dawkins puts forth for 'race' in biology is citing the Edwards 2003 paper trying to establish that race can be used by using ancestry informative markers. However there's one key thing both Dawkins AND Edwards failed to take into account. The markers don't correspond to a definition of race, it's more, geography. In which there's a very tiny amount of genetic material that's concentrated. But we're talking about very, VERY tiny amounts of genetic material. Often, as few as 35 nucleotide markers out of 3.1 billion basepairs are used to identify ancestral continents(Lee, Yin Leng et al. "Comparing Genetic Ancestry and Self Reported Race/Ethnicity in a Multiethnic Population in New York City." 01 Dec 2010. Journal of Genetics (89). Print.) More than likely, they don't even appear in coding regions. Many people have overlapping informative markers in their ancestry. Like..Barrack Obama(Africa AND Europe), or James Watson(Europe, Asia, and Africa).
In fact my own may include up to two to three different continents. They can give you an idea as to where a person's ancestors come from, but it still only has an 85% confidence interval, and it doesn't help to promote a biological basis for race any further, as the studies that attempt to do this use...self identified race. In fact, Rosenburg's 2005 paper goes over this very detail and says, "The arguments about the existence or nonixeistence of 'biological races' are largely orthogonal(irrelevant, or mutually independent) to the question of scientific utility."
Rosenberg, Noah et al. "Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure." 09 Dec 2005. 0668-0669. PLoS Genetics (1). Print.
“One hundred against one.” That was the sentence used by Nazism propaganda to attack the General Theory of Relativity as a “jewish terrorist act” against the “arian physics”. One hundred German scientists disagreed from Einstein. So I'll just paraphrase Einstein's response to this:
“Why 100? One is enough if they're right.”
And I'll go ahead and quote my brother, "So what?"
So...what else ya got? :)
Edit: Oh, and if your stance is really that we don't even have enough information available to define race? Then you can't say it's biological. The time to believe in something is when you have evidence for it.