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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.”

Note by RK ” there is no scientific support for the concept that human populations are discrete, nonoverlapping entities.” – Outside of racist groups, no one, let alone scientists, make such a claim. This article does not debunk the idea that biological groups/races/clades for humans exists: It clearly proves that such groups exists, and shows it in precise detail. However, this data can also debunk racial claims made from people using non-scientific definitions of the word “race”.

When scientists use words like “race”, “populations” or “clades”, these words have precise meanings. Every discovery in biology and evolution over the last 200 years has clearly shown that the basic concept of biological groups has to exist. All forms of life have family trees that develop in ways that can be represented by cladograms, and 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.

Coding weather forcecasting

Coding weather forcecasting

GR2Analyst Tornado GRLEVELX

Intro

articles

Unleash Your Inner Geek With These Excellent Weather Radar Programs

http://thevane.gawker.com/unleash-your-inner-geek-with-these-excellent-weather-ra-1628544982

Sample programs

Gibson Ridge Software, LLC (GRS) was created in March 2005 and produces viewers for weather radar data. GRS applications include GRLevel2 for viewing Level II radar data and GRLevel3 for viewing Level III data. Both viewers feature high speed, high quality radar displays with an intuitive user interface. All GRS applications are written in multithreaded C++ using the base Windows APIs for speed and efficiency.

GRLevelX

ProductsGRLevel3 2.00

GR2Analyst 2.00

GREarth

GRLevel2

 

View storm features in 3D with GR2Analyst’s Volume Explorer

Display 124 nm and 248 nm sweeps for a complete view of hurricanes and other large-scale phenomena

Smoothing reconstructs features distorted by standard bin-oriented displays 

See severe thunderstorm and tornado warnings along with details of Nexrad-identified threats

Learning standards

Massachusetts Earth Science

8.MS-ESS2-5. Interpret basic weather data to identify patterns in air mass interactions and the relationship of those patterns to local weather.

8.MS-ESS2-6. Describe how interactions involving the ocean affect weather and climate on a regional scale, including the influence of the ocean temperature as mediated by
energy input from the Sun and energy loss due to evaporation or redistribution via
ocean currents.

Common Core Math Skills

STANDARD (CCSS.MATH.PRACTICE) INTRODUCTION TO PROGRAMMING THE EV3

MP1 Make sense of problems and persevere in solving them Chapters are all based around solving real-world robot problems; students must make sense of the problems to inform their solutions

MP2 Reason abstractly and quantitatively Programming requires students to reason about physical quantities in the world to plan a solution, then calculate or estimate them for the robot

MP4 Model with mathematics Many processes, including the process of programming itself, must be systematically modeled on both explicit and implicit levels

NGSS

HS-ETS1-2. Design a solution to a complex real-world problem by breaking it down into smaller, more manageable problems that can be solved through engineering.

 

Evolution of cereals and grasses

Evolution of cereals and grasses

Intro (TBA)

Paper 1: “Wheat: The Big Picture”, The Bristol Wheat Genomics site, School of Biological Sciences, University of Bristol

Wheat: The Big Picture – the evolution of wheat

Evolution wheat barley sorghum rice

Figure 2. Phylogenetic tree showing the evolutionary relationship between some of the major cereal grasses. Brachypodium is a small grass species that is often used in genetic studies because of its small and relatively simple genome.

 

Paper 2: Increased understanding of the cereal phytase complement for better mineral bio-availability and resource management

Article (PDF Available) in Journal of Cereal Science 59(3) · January 2013 with 244 Reads
DOI: 10.1016/j.jcs.2013.10.003

Fig-1-Phylogenetic tree of cereals selected grasses PAPhy gene copy numbers

Fig. 1. Phylogenetic tree of cereals and selected grasses. PAPhy gene copy numbers are given for each species and key evolutionary events are indicated.

Paper 2
Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences.
Peng Z, Lu T, Li L, Liu X, Gao Z, Hu T, Yang X, Feng Q, Guan J, Weng Q, Fan D, Zhu C, Lu Y, Han B, Jiang Z – BMC Plant Biol. (2010)

Phylogeny of grasses inferred from concatenated alignment of 43 putative orthologous cDNA sequences

Figure 2: Phylogeny of grasses inferred from concatenated alignment of 43 putative orthologous cDNA sequences. (A) Tree inferred from maximal likelihood method. Bayes inference yielded the same topology. (B) Tree inferred from neighbor joining method. Branch length is proportional to estimated sequence divergence measured by scale bars. Numbers associated with branches are bootstrap percentages. Arabidopsis was used as outgroup. Subfamily affiliation of the grasses is indicated at right.

Paper 3 Evolution of corn

The evolution of maize (corn)

Figure 1: The evolutionary stages of domestication and diversification.
From
Evolution of crop species: genetics of domestication and diversification
Rachel S. Meyer & Michael D. Purugganan
Nature Reviews Genetics 14, 840–852 (2013) doi:10.1038/nrg3605

http://www.nature.com/nrg/journal/v14/n12/fig_tab/nrg3605_F1.html

Paper 4 text

Brachypodium distachyon: making hay with a wild grass
Magdalena Opanowicz, Philippe Vain, John Draper, David Parker, John H. DoonanEmail the author John H. Doonan
DOI: http://dx.doi.org/10.1016/j.tplants.2008.01.007

Phylogenetic Brachypodium and cereals

 

Sonar and ultrasound

Sonar (SOund Navigation And Ranging)

The use of sound to navigate, communicate with, or detect objects – on or under the surface of the water – such as another vessel.

Old Navy Sub sonar GIF

Active sonar uses a sound transmitter and a receiver.

Active sonar creates a pulse of sound, often called a “ping”, and then listens for reflections (echo) of the pulse

Active sonar Wikipedia

Natural sonar

whales

dolphins

echolocation of a dolphin wikipedia

bats

Ultrasound

Medical ultrasound – a diagnostic imaging technique using ultrasound.

Used to see internal body structures such as tendons, muscles, joints, vessels and internal organs.

The practice of examining pregnant women using ultrasound is called obstetric ultrasound.

Ultrasound is sound waves with frequencies which are higher than those audible to humans (>20,000 Hz).

Ultrasonic images also known as sonograms are made by sending pulses of ultrasound into tissue using a probe.

The sound echoes off the tissue; with different tissues reflecting varying degrees of sound. These echoes are recorded and displayed as an image to the operator.

Medical ultrasound (Wikipedia)

Ultrasound human heart 4 chambers Wikipedia

“Amniocentesis is a prenatal test in which a small amount of amniotic fluid is removed from the sac surrounding the fetus for testing. The sample of amniotic fluid (less than one ounce) is removed through a fine needle inserted into the uterus through the abdomen, under ultrasound guidance. The fluid is then sent to a laboratory for analysis. Different tests can be performed on a sample of amniotic fluid, depending on the genetic risk and indication for the test.”

Amniocentesis: WebMD

Amniocentesis image006

 

 

Doppler effect

The Doppler effect

Named after Austrian physicist Christian Doppler who proposed it in 1842.

You hear the high pitch of an approaching ambulance’s siren – and then notice that its pitch drops as it passes you. That’s the Doppler effect.

Listen to the Doppler effect! A passing car beeps its horn

Doppler effect Acela express train

Doppler effect racetrack

The Big Bang Theory – The Doppler Effect

Doppler effect YouTube example 1

Doppler effect YouTube example 2

sound frequency increases during the approach,
is identical as it passes by,
and decreases during the recession.
(Adapted from Wikipedia.)

Watch the spacing of the sound waves, when the car is at rest, and when it is in motion. How does motion change the spacing of the waves?

http://www.acs.psu.edu/drussell/Demos/doppler/doppler.html

doppler-effect-car-frequency

Step 1: Staying at rest

In the center is a stationary sound source.
It produces sound waves.
The wavefronts propagate symmetrically away from the source,
at a constant speed

stationary-sound-source-produces-sound-waves-doppler

 

Step 2: Now the source is moving quickly.

Since the source is moving, the centre of each new wavefront
is slightly displaced to the right.

As a result, the wave-fronts begin to bunch up in front of,
and spread further apart behind, the source.

So an observer in front of the source will hear a higher frequency.

doppler-effect-source-moving-right-mach-0-7

We can see this in water: Doppler effect of water flow around a swan

doppler-effect-of-water-flow-around-a-swan

 

Doppler effect applet

Doppler applet (with sound)

Doppler effect and sonic booms

MCAS problems

By the end of our unit on waves we should be able to do MCAS Physics exam: sample wave problems

 

Learning Standards

2016 Massachusetts Science and Technology/Engineering Curriculum Framework

HS-PS4-1. Use mathematical representations to support a claim regarding relationships among the frequency, wavelength, and speed of waves traveling within various media. Recognize that electromagnetic waves can travel through empty space (without a medium) as compared to mechanical waves that require a medium

SAT subject test in Physics: Waves and optics

• General wave properties, such as wave speed, frequency, wavelength, superposition, standing wave diffraction, and Doppler effect
• Reflection and refraction, such as Snell’s law and changes in wavelength and speed
• Ray optics, such as image formation using pinholes, mirrors, and lenses
• Physical optics, such as single-slit diffraction, double-slit interference, polarization, and color

Code.Org lessons

Hit the ground running with coding lessons from Code.Org, using the Blockly coding language.

 

code-org-puzzle-coding-example

 

What are “conditionals”?

https://www.flocabulary.com/lesson-plan-coding-conditionals/

“On One Condition” If-then-else conditional flowchart lesson

 

Course 2. Stage 3: Angry Birds coding the path through the maze.

Course 2, Stage 6: Maze Loops

Course 2, Stage 7. Artist loops

Course 2, Stage 8. Bee Loops.

Course 2, Stage 10. Bee Debugging.

Course 2, Stage 11. Artist debugging.

Course 2, Stage 13. Bee Conditionals.

Course 2, Stage 16. Flappy Birds

 

Code.org Stage 19 Artist – nested loops
Code.Org: Course 4 Intro to programming

 

Course 4: Stage 6, Artist variables
Course 4, Stage 7 : Play Lab variables

 

Course 4, Stage 9. Bee “For” loops, and counters
Course 4, Stage 10. Artist. “For” Loops.

 

Course 4. Stage 11. Play Lab “For” loops
Course 4. Stage 12. Artist Functions
Homework: Write a paragraph explaining how loops work, how WHILE loops work,
and how DO…WHILE loops work.
Tutorialspoint: Loops and Chapter 8: Loops. Introduction to Programming


Course 4. Stage 14. Artist with parameters
Course 4. Stage 16. Bees – Functions with parameters
Homework: What is a “Hello, World!” program?
Excelwithbusiness.com: Say “Hello, world!”.
How would  we tell a computer to write “Hello, World!” in Blockly?
PCAdvisor How to code-with-google-blockly


Course 4, Stage 19: variables super challenge
Homework :Go to TutorialsPoint (link below) Choose “programming environment”.
(1) What’s the purpose of a text editor?
(2) What’s the purpose of a compiler?
(3) What’s the purpose of  an interpreter?
Tutorialspoint.com lessons

 

Course 4. Stage 20. For Loops Super Challenge: Can you get Skrat to his acorn using as few blocks as possible?

Course 4. Stage 21. Super Challenge – Functions and Parameters

Course 4. Stage 2. EXTREME CHALLENGE. No rules. No clues. Just the challenge!

Primary resources:
Code.Org: Course 2 Intro to programming and Accelerated Intro to Computer Science: Code.Org

Hexadecimal

The hexadecimal numeral system, hex, is a numeral system made up of 16 symbols (base 16).

Your standard numeral system is called decimal (base 10) and uses ten symbols: 0,1,2,3,4,5,6,7,8,9.

Hexadecimal uses the decimal numbers and six extra symbols, from the English alphabet: A, B, C, D, E and F.

Hexadecimal A = decimal 10, and hexadecimal F = decimal 15.

We mostly use the decimal system. This is because humans have ten fingers (ten digits). Computers however, only have on and off, called a binary digit (or bit, for short). A binary number is just a string of zeros and ones: 11011011, for example.

For convenience, engineers working with computers tend to group bits together. In earlier days, such as the 1960’s, they would group 3 bits at a time (much like large decimal numbers are grouped in threes, like the number 123,456,789).

Three bits, each being on or off, can represent the eight numbers from 0 to 7: 000 = 0; 001 = 1; 010 = 2; 011 = 3; 100 = 4; 101 = 5; 110 = 6 and 111 = 7. This is called octal.

As computers got bigger, it was more convenient to group bits by four, instead of three. The additional bit can be either on or off, a 0 or a 1. So this doubles the numbers that the symbol would represent. This is 16 numbers.

Hex = 6 and Decimal = 10, so it is called hexadecimal.

Four bits is called a nibble (sometimes spelled nybble). A nibble is one hexadecimal digit, and is written using a symbol 0-9 or A-F.

Two nibbles is a byte (8 bits). Most computer operations use the byte, or a multiple of the byte (16 bits, 24, 32, 64, etc.).

Hexadecimal makes it easier to write these large binary numbers.
To avoid confusion with decimal, octal or other numbering systems, hexadecimal numbers are sometimes written with a “h” after the number. For example, 63h means 63 hexadecimal. Software developers quite often use 0x before the number (0x63).

Adapted from https://simple.wikipedia.org/wiki/Hexadecimal_numeral_system

How to Convert from Decimal to Hexadecimal: WikiHow