Evolution Runs Faster on Short Time Scales — Via Quanta Magazine

“Think of it like the stock market,” he said [Simon Ho]. Look at the hourly or daily fluctuations of Standard & Poor’s 500 index, and it will appear wildly unstable, swinging this way and that. Zoom out, however, and the market appears much more stable as the daily shifts start to average out. In the same way, the forces of natural selection weed out the less advantageous and more deleterious mutations over time.”
Classwork:
Read the article titled: Evolution Runs Faster on Short Time Scales (Quanta Magazine, March 14, 2017)
Advertisements

AMGEN Biotech Experience, 2017

Maler_der_Grabkammer_des_Sennudem_001

Ploughing with a yoke of horned cattle in Ancient Egypt. Painting from the burial Chamber of Sennedjem, c. 1200 BC

 

Although the word biotechnology sounds new and contemporary, we’ve been tweaking genes–the stuff of life–for millennia:
“Early people began altering communities of flora and fauna for their own benefit through means such as fire-stick farming and forest gardening very early. Exact dates are hard to determine, as people collected and ate seeds before domesticating them, and plant characteristics may have changed during this period without human selection. An example is the semi-tough rachis and larger seeds of cereals from just after the Younger Dryas (about 9,500 BC) in the early Holocene in the Levant region of the Fertile Crescent. Monophyletic characteristics were attained without any human intervention, implying that apparent domestication of the cereal rachis could have occurred quite naturally. 
Agriculture began independently in different parts of the globe, and included a diverse range of taxa. At least 11 separate regions of the Old and New World were involved as independent centers of origin. Some of the earliest known domestications were of animals. Pigs were domesticated in Mesopotamia around 13,000 BC. Sheep were domesticated in Mesopotamia between 11,000 and 9,000 BC. Cattle were domesticated from the wild aurochs in the areas of modern Turkey and Pakistan around 8,500 BC. Camels were domesticated late, perhaps around 3,000 BC.”–Via
Nowadays, the stuff that we can do with genes would seem like wizardry to ancient Mesopotamians. We can use the immune system of bacteria to edit the human genome. With current techniques, insulin can be made by embedding human genetic code in the genome of Escherichia coli. In other words, if the plow, the scythe, and slashing and burning were the tools that made it possible for the ancients to manipulate genes, the micropipette, the electrophoresis chamber, and the agarose gel are new the hardware.
 AP and Honor (10th Grade) students:
Write a brief reflection–of no more than 150 words–of your Biotech Experience (March 6–10, 2017) on the comment section below. This being a blog, you can add pictures, videos, and/or hyperlinks to your comment. Remember that your experience had to be documented with pictures (a minimum of 5). Send them to madrover@cupeyvilleschool.org. The total value of this assignment is 50 points. Due date: March 31, 2017.

Gattaca & Bioethics

I saw Gattaca for the first time during the late 90’s. The Human Genome Project was all over the news. Bitch & Tubthumping received–unfortunately–a lot of radio-play; social media did not exist; and the Internet was in its infancy (People had to wait over 30 minutes to download a song). I was in my senior year, and it was a great time for scifi–The Matrix was blowing people’s minds as well. Like a lot of good science fiction, Gattaca points its finger to the present; the film mirrors much of the current zeitgeist. A lot has happened since 1997, but Niccol’s vision still speaks volumes about current research and bioethics; it does so poetically and politically.
Classwork
An essay/review will be assigned–it will be submitted to a Turn it in assignment. Meanwhile, I want you to think about the film. I’ve listed quotes, statements, and ideas for that purpose. Your task will be to write a comment–of no more than 150 words–based on at least 3 elements from the list:
“A genetic quotient second to none”. 
“Genoism is called”. 
Research the concepts: Social DarwinismEugenics, and Dystopia.
“Borrowed ladder” and “de-gene-erate”. 
“This guy’s helix tucked under your arm” — aligned to Chapter 13: The Molecular Basis of Inheritance. 
“Are you color blind too, Vincent” — aligned to Chapter 12: The Chromosomal Basis of Inheritance. 
“You could conceive naturally 1,000 times and never get such a result” — aligned to Chapter 12: The Chromosomal Basis of Inheritance. 
The listed concepts, quotes, and ideas can serve as the basis for your work, but keep in mind that they are suggestions. Your post has to be written in the comment section of this blog, and it counts as a comment for your semester-long project. Clicking the hyperlinks is encouraged. The guidelines for this assignment are the same ones that we follow for all comments. You can re-visit the rubric at Edline. This is classwork; it must be done individually, and it has a value of 15 points. 

Blood Typing — The Game

a2ba760f9ad9d2706a2deb6cb892cf5e

Skin wound: colored platelets, fibrin mesh (clotting), leukocites & erithrocites

Yesterday we talked about multiple alleles, an update to Mendel’s Laws. Classical genetics can explain inheritance patterns of blood types. We’ve come a long way. Blood transfusions are as common as insulin pumps — these biomedical breakthroughs resulted in multiple Nobel Prizes:
Before Nobel Prize awarded Karl Landsteiner discovered the ABO human blood groups in 1901, it was thought that all blood was the same. This misunderstanding led to fatal blood transfusions. Later, in 1940, Landsteiner was part of discovering another blood group, the Rh blood group system. There are many blood group systems known today, but the ABO and the Rh blood groups are the most important ones used for blood transfusions. The designation Rh is derived from the Rhesus monkey in which the existence of the Rh blood group was discovered.
To find out more about the behavior of human blood phenotypes, click on this link to play & learn…
Homework for Monday, Jan 23, 2017:
Read the tutorials before playing the game. All of them: What is a blood type?; How do you determine a patient’s blood type?; How do you perform safe blood transfusions; and About the game. Bring laptops and/or devices to class. We will play the game with specific instructions. This activity will be part of your Lab grade for Sem. II, 2016-2017. 

Iguana vs snakes, via Planet Earth II

iguana
I found myself screaming & cheering out loud for this guy.
“It’s hard to find people who were cheering on the snakes of Fernandina island during Sunday night’s episode of Planet Earth II. In the standout scene of the show, one baby iguana, just hatched, starts its run as dozens of chaser snakes emerge, like ropes thrown out of the rocks, slaloming across the shingle, red tongues zipping and unzipping mouth holes.” — Via

A heartbeat in a chip

““This new programmable approach to building organs-on-chips not only allows us to easily change and customize the design of the system by integrating sensing but also drastically simplifies data acquisition,” said Johan Ulrik Lind, first author of the paper, postdoctoral fellow at the Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS), and researcher at the Wyss Institute for Biologically Inspired Engineering at Harvard University.””–Via The first fully 3-D printed-heart-on-a-chip

A pic of Panthera uncia — via N7_Nate

About the snow leopard’s habitat:
It would be one of the 10 largest countries in the world. It also would be the 6th least dense country in terms of human population. It is the birthplace of many of the world’s greatest rivers – the Yangtse, Yellow, Ganges, Indus, Amu Darya, and others – that provide life-sustaining water to hundreds of millions of people. All of the mountains on earth that soar above 7,000 meters (23,000 feet) – well over 100 of them – are found here.
This huge, remote, and incredible region is the home to the snow leopard.
About the threats that snow leopards face: 
Poaching (mostly for skins) and retaliatory killing (by shepherds after predation of livestock by snow leopards) were long suspected as the leading threat to these big cats, and a just-published study from TRAFFIC supports the belief that this may be leading to a decline in the snow leopard population.
The loss of wild prey, the great mountain goats and sheep that Schaller dubbed “mountain monarchs,” from overhunting and livestock impacts (competition, overgrazing, disturbance, and even disease) is also significant. Development in these high mountains is a slow and difficult task, but new roads are increasing access and the ability for mines and other extractive industries to reach the snow leopard’s home.
[h/t]

No Man’s Sky & Maths

A lot of people hate this game. I love it enough to post a picture of me playing it.

A lot of people hate this game. I love it enough to post a picture of me playing it.

We’ve been talking about huge numbers lately. One example of many would be the amount of polymers that exists inside a cell. But we’re also discussing small numbers; they help us make sense of how small a peptide is. The thing is–numbers are important. We can measure & count because of them. With numbers we can describe the curvature of a sphere–a model for a planet or a cell. Chapter 4 of our textbooks has shown us that with math, we can say how much membrane the cell needs to properly function–how much volume to surface ratio our cells need. In Biology we cannot avoid numbers and patterns.
Use no more than a sentence for each of the following * —
a) research the game No Man’s Sky (Hello Games, 2016);
b) find out what is an algorithm;
c) define the word fractal; 
d) who was Aristid Lindenmayer?;
e) and, finally: how many zeroes are there in a quintillion?
*Whoever answers all of these questions first, will get a 5 point bonus for Test III.

Palindromes & nucleotides (or how to edit genes with the syntax of life)

art-of-the-cell-crispr-cas9-in-complex-with-guide-rna-and-target-dna
The CRISPR/Cas system (Clustered regularly interspaced short palindromic repeats) is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages, and provides a form of acquired immunity. [Image via. Text via]
We’ve discussed the chemical nature of life; which is all about molecules capable of forming an increasingly complex–and almost infinite–set of bio-machines. In other words, the stuff of life is all about the right chemistry–for example, polymers that can store and manage information.
All life on Earth can do this, thanks to nucleic acids. The following 16 minute film shows what these molecules have been doing for millions of years, in order to defend bacteria from their oldest foe–which is ours as well–the virus. Scientists have harnessed this bio-molecular immune system, and used it to edit, remix, and shuffle our own nucleic acids.
Keep in mind that many things about this video will become clearer during the 2nd semester of AP Bio. Nevertheless, I highly recommend watching the film with everything we have said about bio-molecules–especially nucleic acids & polypeptides–in mind: