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Genetic variation, classification and race
Genetic variation, classification and ‘race’
Lynn B Jorde & Stephen P Wooding
Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
Nature Genetics 36, S28 – S33 (2004) Published online: ; | doi:10.1038/ng1435
New genetic data has enabled scientists to re-examine the relationship between human genetic variation and ‘race’. We review the results of genetic analyses that show that human genetic variation is geographically structured, in accord with historical patterns of gene flow and genetic drift.
Analysis of many loci now yields reasonably accurate estimates of genetic similarity among individuals, rather than populations. Clustering of individuals is correlated with geographic origin or ancestry. These clusters are also correlated with some traditional concepts of race, but the correlations are imperfect because genetic variation tends to be distributed in a continuous, overlapping fashion among populations. Therefore, ancestry, or even race, may in some cases prove useful in the biomedical setting, but direct assessment of disease-related genetic variation will ultimately yield more accurate and beneficial information.
Figure 1: A neighbor-joining network of population similarities, based on the frequencies of 100 Alu insertion polymorphisms.
The network is rooted using a hypothetical ancestral group that lacks the Alu insertions at each locus. Bootstrap values are shown (as percentages) for main internal branches. (Because of the relatively small sample sizes of some individual populations, bootstrap values for terminal branches within main groups are usually smaller than those of the main branches, indicating less statistical support for terminal branches.)
The population groups and their sample sizes are as follows:
Africans (152): Alur, 12; Biaka Pygmy, 5; Hema, 18; Coriell Mbuti Pygmy, 5; a second sample of Mbuti Pygmy from the Democratic Republic of the Congo, 33; Nande, 17; Nguni, 14; Sotho/Tswana, 22; Kung (San), 15; Tsonga, 14. East Asians (61):
Cambodian, 12; Chinese, 17; Japanese, 17; Malay, 6; Vietnamese, 9. Europeans (118): northern Europeans, 68; French, 20; Poles, 10; Finns, 20. South Indians (365): upper caste Brahmin, Kshatriya and Vysya, 81; middle caste Kapu and Yadava, 111; lower caste Relli, Mala and Madiga, 74; tribal Irula, Khonda Dora, Maria Gond and Santal, 99.
Figure 2
A neighbor-joining tree of individual similarities, based on 60 STR polymorphisms, 100 Alu insertion polymorphisms, and 30 restriction site polymorphisms.
The percentage of shared alleles was calculated for all possible pairs of individuals, and a neighbor-joining tree was formulated using the PHYLIP software package. African individuals are shown in blue, European individuals in green and Asian individuals in orange.
Figure 3
(a) Results of applying the structure program to 100 Alu insertion polymorphisms typed in 107 sub-Saharan Africans, 67 East Asians and 81 Europeans. Individuals are shown as dots in the diagram.
Three clusters appear in this diagram; a cluster membership posterior probability of 100% would place an individual at an extreme corner of the diagram.
(b) A second application of the structure program, using the individuals shown in a as well as 263 members of caste populations from South India. Adapted from ref. 32.
Figure 4
A neighbor-joining tree formulated using the same methods as in Figure 2, based on polymorphisms in the 14.4-kb gene AGT.
A total of 246 sequence variants, including 100 singletons, were observed. The 368 European, Asian and African individuals are described further in ref. 54.
Author’s conclusion: “Race remains an inflammatory issue, both socially and scientifically. Fortunately, modern human genetics can deliver the salutary message that human populations share most of their genetic variation and that there is no scientific support for the concept that human populations are discrete, nonoverlapping entities.
Furthermore, by offering the means to assess disease-related variation at the individual level, new genetic technologies may eventually render race largely irrelevant in the clinical setting. Thus, genetics can and should be an important tool in helping to both illuminate and defuse the race issue.”
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Note by RK about -> ” there is no scientific support for the concept that human populations are discrete, nonoverlapping entities.”
– Outside of racist groups, no scientist even makes such a claim. This article does not debunk the idea that biological groups for humans exists: It clearly shows that such groups exist, in precise detail. However, this data debunk claims made from people using non-scientific definitions of words.
When scientists use words like “race”, “population” or “clade”, these words need to have precise meanings. Every discovery in biology and evolution over the last 200 years shows that biological groups has to exist. That is to say, all life has a family tree that can be represented by cladograms. Those cladograms show evolutionary phylogenies.
“A clade is a grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor. Using a phylogeny, it is easy to tell if a group of lineages forms a clade. Imagine clipping a single branch off the phylogeny — all of the organisms on that pruned branch make up a clade.”
See Clades and phylogenies and clades rotate = equivalent phylogenies.
Related articles
The Importance of Race and Ethnic Background in Biomedical Research and Clinical Practice
The New England Journal of Medicine, Vol. 348, p. 1170-1175, 2003
Esteban González Burchard, M.D., Elad Ziv, M.D., Natasha Coyle, Ph.D., Scarlett Lin Gomez, Ph.D., Hua Tang, Ph.D., Andrew J. Karter, Ph.D., Joanna L. Mountain, Ph.D., Eliseo J. Pérez-Stable, M.D., Dean Sheppard, M.D., and Neil Risch, Ph.D.
The Genomic Challenge to the Social Construction of Race
By Jiannbin Lee Shiao, Thomas Bode, Amber Beyer et al, Sociological Theory, Vol 30, Issue 2, 2012
Race in biology, genetics and cladistics. Wikipedia.
The Whole Side of It—An Interview with Neil Risch. By Jane Gitschier
Scaling and biophysics
From Math Bench Biology Modules:
Scaling examines how form and function change as organisms get larger – in other words, how do biological features scale across size? Do they change in meaningful ways as organisms get bigger or smaller? Of course, you can’t even ask these types of questions without having a way of measuring how relationships change mathematically.
Why study these relationships? Well, if you understand how form or functions change as organisms get bigger or smaller, it is possible to learn something fundamental about what underlies the processes or learn about what factors place evolutionary limits on organism growth and adaptations. For instance, determining at what size arthropods can no longer support the weight of their exoskeleton gives us clues about the limits of their growth.
Let’s use a concrete example so you’ll know what we mean. Here is some data on body size and metabolic rate for mammals….
- metabolic rate increases as animals get bigger. That’s because we are specifically interested in total energy consumed (here measured through oxygen consumption). Of course, bigger animals will use more oxygen than smaller ones (think about how big a breath a lion takes compared to a mouse).
- But look at the values adjusted for body size (the last value listed for each species). Mice use a lot more oxygen per gram than a lion. This means that lions use oxygen more efficiently than mice.
- As mammals get bigger, this increase in efficiency is not linear (notice how the steepness of the slope decreases as size increases).
- This means that metabolism does not scale linearly with body size.
“Who cares?” Well, it turns out that how metabolism (and other factors) scales with body size can give important information about which factors are most important in limiting these biological functions. If we can understand that, we understand a lot more about biology!
Math Bench Biology Modules, University of Maryland: Scaling and Power laws
– – –
How scaling affects biology
There are species of animals such as the deer and the elk that are closely related but of different size. Galileo took notice that the bones of the elk are not just proportionally thicker to the bones of the deer – but instead the elk’s bones are even much thicker.
The elk’s bone has to be much thicker to lower the stress in the bone below the breaking point of the bone. Even so, elk and all the other large vertebrates are still more likely of breaking their bones than the more active smaller animals.
http://www.dinosaurtheory.com/scaling.html
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External links
http://www.av8n.com/physics/scaling.htm
The Principle of Scale: A fundamental lesson they failed to teach us at school
The Biology of B-Movie Monsters, Michael C. LaBarbera
Scaling: Why Giants Don’t Exist, Michael Fowler, UVa 10/12/06
Science of Jurassic Park
Jurassic Park is a 1993 film directed by Steven Spielberg. The first installment of the Jurassic Park franchise, it is based on the 1990 novel of the same name by Michael Crichton.
Next Generation Science Standards: Science & Engineering Practices
● Ask questions that arise from careful observation of phenomena, or unexpected results, to clarify and/or seek additional information.
● Ask questions that arise from examining models or a theory, to clarify and/or seek additional information and relationships.
● Evaluate a question to determine if it is testable and relevant.
● Ask and/or evaluate questions that challenge the premise(s) of an argument, the interpretation of a data set, or the suitability of the design
Science and engineering practices: NSTA National Science Teacher Association
Next Gen Science Standards Appendix F: Science and engineering practices
1. When did dinosaurs live? Investigate the geological eras.
Another view of the relationship between geological eras and the Earth’s strata.
2. What are chromosomes/genes/DNA nucleotides?
DNA is like an alphabet: Analogies to explain nucleotides, genes and chromosomes
3. How might DNA possibly be preserved for long periods of time?
4. What is the scientific premise of the film: How did they recreate ancient dinosaurs? Did they (according to the film) create dinosaurs at all?
5. According to the book & film, not enough intact DNA was recovered to create a true dinosaur. How then were the theme park dinosaurs created?
http://jurassicpark.wikia.com/wiki/Filling_the_sequence_gaps
6. Have scientists ever actually discovered preserved soft tissue, and/or protein, in dinosaur fossils?
http://www.livescience.com/41537-t-rex-soft-tissue.html
http://www.smithsonianmag.com/science-nature/dinosaur-shocker-115306469/?no-ist
https://student.societyforscience.org/article/more-dinosaur-bones-yield-traces-blood-soft-tissue
7. Have scientists ever actually discovered preserved DNA in dinosaur fossils?
http://www.livescience.com/23861-fossil-dna-half-life.html
http://www.sci-news.com/paleontology/science-dinosaur-dna-amber-01383.html
http://scitechdaily.com/researchers-calculate-that-dna-has-a-521-year-half-life/
http://www.nature.com/news/dna-has-a-521-year-half-life-1.11555
https://en.wikipedia.org/wiki/Ancient_DNA
8. Some scientists have proposed that we can realistically reverse engineer dinosaurs from living birds. What is their biological, and evolutionary reasoning for why this could make sense?
http://www.livescience.com/17642-chickenosaurus-jack-horner-create-dinosaur.html
Can Scientists Turn Birds Back Into Dinosaur Ancestors? National Geographic
TED Talks: Jack Horner on building a dinosaur from a chicken
9. How would these scientists actually go about doing this? (Summarize in a clearly written paragraph, describing several steps.)
Additional resources
Are Movies Science? DINOSAURS, MOVIES, AND REALITY Univ. of California Museum of Paleontology
Real-Life ‘Jurassic World’ Dinos May Be Possible, Scientist Says: LiveScience
Can scientists clone dinosaurs? How Stuff Works
Scrappy Fossils Yield Possible Dinosaur Blood Cells: National Geographic
DNA has a 521-year half-life, Nature (scientific journal)
The final nail in the Jurassic Park coffin. Research just published in the journal The Public Library of Science ONE (PLOS ONE)
Absence of Ancient DNA in Sub-Fossil Insect Inclusions Preserved in ‘Anthropocene’ Colombian Copal. (scientific journal)
Science of Jurassic Park: JurassicWikia
Book: The Science of Jurassic Park: And the Lost World Or, How to Build a Dinosaur
Are we consuming too little salt?
…Cutting back on salt can reduce blood pressure, but often, the change in blood pressure is small. According to the American Heart Association, a person who reduces salt intake from median levels (around 3,400 milligrams ) to the federal recommended levels (no more than 2,300 mg) typically sees a slight drop of 1% to 2% in blood pressure, on average.
Also, other factors affect blood pressure. For example, blood pressure increases with weight gain and decreases with weight loss. So, keeping a healthy weight can help prevent high blood pressure. Eating foods high in potassium also seems to counter some of the effects of high salt consumption on blood pressure.
Studies comparing salt intake in different countries worldwide have not found a clear connection between salt intake and high blood pressure. Societies that eat lower levels of salt do not necessarily have less heart disease than those that eat a lot of salt.
…Surprisingly little is known about how much salt we need. U.S. residents consume, on average, about 3,400 milligrams of salt per day. For decades, the U.S. government and organizations, such as the American Heart Association, have recommended people consume less salt. Current dietary guidelines recommend no more than 2,300 mg of sodium—about a teaspoon of salt—per day for teens and adults. No more than 1,500 mg per day is recommended for groups at higher risk of heart disease, including African Americans and everyone over the age of 50.
The U.S. dietary guidelines were established in the 1970s when relatively little information was available about dietary salt and health. The guidelines were the best guess, given the information available at the time. …
Some scientists now say that the average amount of salt U.S. residents eat (3,400 mg of salt per day) is safe and may even be healthier than the lower government guidelines.
In fact, a study found that people who meet the U.S. recommended limits for salt (2,300 mg of sodium per day) have more heart trouble than those consuming more salt. This study included approximately 150,000 people from 17 countries and was published in the New England Journal of Medicine.
Scientists challenging the current guidelines say people should consume at least 3,000 mg of salt per day and up to 6,000 mg per day. The new research results suggest a low-sodium diet may stimulate the production of renin, an enzyme released by the kidneys. Renin plays a role in regulating the body’s water balance and blood pressure. Too much renin may harm blood vessels, and a high-sodium diet would help lower the amount of renin produced….
KaiserScience 