Building Build, Thyself

“Good buildings come from good people, and all problems are solved by good design.”
Stephen Gardiner

Years ago, when I was in graduate school, an IT technician was repairing the lab internet. He asked me, “So when will we be able to grow cars?”  The first thing that popped into my mind was how complex a modern car is.  According to Toyota, a modern car is made up of 30,000 parts if you count down to the bolts.  Electric vehicles don’t have as many “parts” according to an article in Handelsblatt Today, an electric car has 200 parts while a gas or diesel car has more than a 1000 parts.  I answered, “It will be quite some time before we can grow a car.  There is still a lot of work to do.”

It might seem strange to ask “about growing cars”; however, writers fill science fiction with the unbelievable.  In the television show Earth: final conflict, the alien Taelons grew buildings. The Leviathans are living spaceships in the television series FarScape. While a science fiction show is not the best barometer for what is possible, it’s not a measure of the imposable either.  When the television show Star Trek debut in 1966, most of the technology seemed imposable.  However, a lot of “Star Trek” technology exists now.  Google translate, while not perfect, makes a passable universal translator.  We also have handheld communicators (cell phones) and tablet computers.  There is even a subset of 3D printers that focus on food (the replicator.)

Technology tends to make truth out of our imagination. That technology is often driven by challenging scientific endeavors.  One of the most complex scientific efforts currently being pursued is sending people to Mars.  One of the biggest problems is providing astronauts with safe housing.  Beyond the extremely thin atmosphere on Mars, the surface of the planet has two other significant issues, the temperature, and the surface radiation.  The average daily temperature of Mars is -81° F (-63° C).  While the average yearly surface radiation on Mars is eight rads, on earth, its 0.63 rads.

The surface of Mars is lethal to astronauts.  Currently, the “best” idea for providing protective habitats for astronauts is to bury the habitat under several feet of Martian soil.  The Martian soil would provide insulation and protect against radiation.   However, burying the habitats would require large equipment so that the astronauts can move large quantities of soil. Alternatively, we could send prebuilt habitats with walls that are highly insulated and resistant to radiation.  The exact thickness and weight of the habitats would depend on the material used.

The biggest problem with these ideas is the weight. Either the habitat or the equipment to build the habitat weighs a lot.  It is both expensive and difficult to transport heavy objects.  According to NASA, it currently costs $10,000 per pound to put an object into earth orbit.

So, what does science fiction technology, questions about growing cars, and visiting Mars have to do with each other?  Well, science is again working towards making science fiction reality.  NASA scientists are researching the possibility of using fungus (mushrooms) to grow buildings.  When we think of fungus, especially mushrooms, what you generally picture is just a small part of the whole organism, the fruiting body.  The fruiting body of the mushroom produces mushroom spores and allows the fungus to spread.

The bulk of the mushroom grows underground or inside a decaying log and is called the mycelium, which is a fibrous material composed of hyphae fibers.  The idea is that engineers will seed lightweight shells with spores and dried food.  Then when the structures reach their destination water, collected from the local environment would activate the spores, which grow filling the shell creating rigid, durable, and insulated buildings.

When the building is full-grown, withholding water and nutrients will stop the growth.  Later if the structure is damaged, astronauts can add water and nutrients, and the building will repair itself. Using biologicals materials like funguses to build buildings would have an additional advantage for places like Mars.  If you want to expand a building, add another shell filled with water and nutrients, the mycelium from the old structure will grow into and fill the new one.

The final advantage of biological buildings is that once they are no longer needed or reach the end of their life, they can be composted and used to either make new buildings or grow crops.  Reusing the fungus as nutrients will reduce the production of waste materials and make the site more efficient.

Additionally, using techniques like CRISPR, the Mycelium could be engineered to secret natural resins or rubbers, turning them into complex composite materials. It is even possible that eventually, we could engineer the fungus to grow into specific shapes.   Imagine a giant puffball mushroom engineered to grow into a hollow sphere 10-12 feet in diameter.

In addition to using fungus, other groups are exploring the use of other organisms to build buildings.  A group out of the University of Colorado at Boulder has developed a method using cyanobacterium.  The researchers’ mix cyanobacterium, gelatin, and sand together into a brick-shaped mold.  The bacteria grow into the gelatin, where it uses light and CO2 to produce calcium carbonate.  The result is a rigid cement-like brick after all calcium carbonate is one of the components of cement. 

Additionally, the bricks can heal themselves if cracked or even reproduce themselves if broken in half.   The researches cut bricks in half placed half back in the mold with more gelatin and sand, and the bacteria reformed the brick.

While I don’t expect to be living in a house, I grew myself anytime soon. It is starting to look like science will again make science fiction a reality.  While most of what scientists are developing is for use in resource-poor areas like the moon or Mars. We will see offshoots of this technology in use here on earth.  For instance, the bricks created by cyanobacterium absorb CO2 from the environment, unlike regular cement, which produces CO2.

Additionally, the company Basilisk out of the Netherlands is already selling self-healing concrete, which uses calcium carbonate producing bacteria.  For schools and universities, there is a tremendous research opportunity.  While researchers have established the basic idea behind biological building materials, there is still a lot to learn.  For example, there are large numbers of microorganisms that deposit minerals, which ones work best.  Does a mix of multiple microbes work better than one?  What is the most efficient sand size is it only one size or various sizes? This type of research that involves testing thousands of small permutations is perfect for undergraduate researchers and undergraduate classes.

I don’t know what effect all these biological materials will have on construction, but I’m sure it will be fascinating.  Maybe next time someone asks me, “when will we grow cars?” I will tell them, “I’m not sure, but I can grow your garage.”

Thanks for Listing to My Musings
The Teaching Cyborg

How Genetic Engineering Should Be Done

“As medical research continues and technology enables new breakthroughs, there will be a day when malaria and most all major deadly diseases are eradicated on Earth.”
Peter Diamandis

It seems that I have written about genetic engineering in humans a lot.  Most of the writing has focused on Dr. He Jiankui and his experiments to produce humans genetically resistant to HIV.  For a while, it was not even clear where Dr. Jiankui was, though he was said to be under house arrest. On January 3, 2020, Nature published a news article, “What CRISPR-baby prison sentences mean for research.” This article adds several pieces of information to the CRISPR-baby story.  First, China has confirmed that there was an additional birth.  Dr. Jiankui had previously stated that a second woman was pregnant.  However, the mother was in the earliest stages, so it was not clear whether the pregnancy would carry to term.  We now know that a third child was born.

Second, Chines news announced that Dr. Jiankui and two of his colleges were convicted.  The Chines court said, “in the pursuit of “fame and profit,” He and two colleagues had flouted regulations and research and medical ethics by altering genes in human embryos that were then implanted into two women.” Dr. Jiankui received the most severe sentence of three years in prison while his calibrators received shorter sentences.

While some scientist thinks this is a positive step. “Tang (a science-policy researcher at Fudan University in Shanghai) says the immediate disclosure of the court’s result demonstrates China’s commitment to research ethics. This is a big step forward in promoting responsible research and the ethical use of technology, she says.”  Lu You another scientist worries this could negatively impact other research into CRISPR mediated social health care. “If I were a newcomer, a researcher wishing to start gene-editing research and clinical trials, the case would be enough to alert me to the cost of such violations.”

I suspect that a lot of people will find it surprising that after the controversy over Dr. Jiankui’s use of CRISPR to engineer babies that there is any work going on using CRISPR and humans.  However, not only is their research into using CRISPR to treat human disease, some of this research has reached the stage of clinical trials.  Additionally, this use of CRISPR is a whole different animal from Dr. Jiankui’s work. Now that we have reached the end of Dr. Jiankui’s story, let’s talk about how to do human genetic engineering correctly.

First, when it comes to human genetic engineering, there are two general classifications, heritable and nonheritable. As the name implies heritable means, it can be passed on to children and released into the general population.  In nonheritable genetic engineering, parents cannot pass the genetic changes to their offspring.  In general, the difference between heritable and nonheritable genetic engineering is the cells that scientists genetically engineer.  The nonheritable engineering usually uses cells taken from an adult often adult stem cell.  In both cases, we will be discussing the use of CRISPR to modify adult blood stem cells.

Blood is composed of four components, red blood cells, white blood cells, platelets, and plasma.  The four types of blood cells have a finite lifetime, and the body continually replaces them.  The body uses stem cells to produce new blood cells.  For example, a red blood cell also known as an erythrocyte, develops from the common myeloid progenitor cell (Figure 1 B).  The common myeloid progenitor cell develops from the Hemocytoblast (Figure 1 A), which is a multipotent stem cell.  Hemocytoblasts are a stem cell because when it divides one of the daughter cells regenerates the Hemocytoblast while the other daughter develops into a mature cell type like an erythrocyte.  It is a multipotent stem cell because its progeny can develop into multiple types of cells (Figure 1 D1-10).

A basic diagram of hematopoiesis. Image modified from Hematopoiesis simple.png by Mikael Häggström. Creative Commons Attribution-Share Alike 3.0 Unported.
A basic diagram of hematopoiesis. Image modified from Hematopoiesis simple.png by Mikael Häggström. Creative Commons Attribution-Share Alike 3.0 Unported.

In addition to regenerating themselves and producing a differentiating daughter cell, hemocytoblasts can divide to produce two hemocytoblasts.  Since hemocytoblasts can produce two hemocytoblast stem cells, scientists can expand populations of hemocytoblasts.  The ability to expand the stem cells makes them particularly useful for genetic engineering.

Hemocytoblasts can be clonally grown in culture in a lab.  Growing cells clonally means that the population starts from a single cell. Therefore, all the cells are genetically identical.  The specifics of clonal cell culture are not essential to this article, but you can read the basics here. Clonal cell culture gives us the first advantage over embryotic genetic engineering.  When scientists genetically engineer an embryo, the only way to know if the change was successful in all the cells is to test all the cells, which will destroy the embryo.  With clonal cells, you can test as many of the cells as you want and grow more.  Additionally, since the cells are clonal, you know all the cells in the population are genetically the same. 

The other advantage of genetically engineered hemocytoblasts is that they can be transplanted into patients using the techniques for bone marrow transplantation, which brings us to the current generation of CRISPR mediated medical treatments.

The first clinical trial using CRISPR was carried out by oncologist Lu You at Sichuan University in Chengdu, China.  The plan was to use CRISPR to increase the immune system’s response to aggressive lung cancer.  The researchers removed cells from the patents and then disabled the PD-1 gene, which should enhance the immune response.  Dr. You is currently working on a manuscript describing the results of his work. This experiment is not a surprise; genetic engineering of immune cells for the treatment of cancer has a long history.  What CRISPR has added to the technique is a faster, more accurate way to change the cells.

In addition to the cancer work in China, the US has also approved CRISPR mediated medical treatment.  The treatment we know the most about involves Victoria Gray, who suffers from sickle cell anima.  Sickle cell anime is a painful, debilitating disease that causes red blood cells to become misshapen and sticky.  Victoria Gray volunteered to have her blood stem cells engineered so that the red blood cells express fetal hemoglobin which the doctors hope will compensate for the defective adult hemoglobin that causes sickle cell anima.  Victoria received the transfusion of genetically edited cells early this summer (2019) and the results are quite promising.  Doctors will follow Victoria’s progress for months perhaps even decades.  The researchers will also have to repeat the treatment with additional patients.  Using gene editing to treat sickle cell anime is by no means a done deal but for the first-time individuals that suffer from the illness might have a real permeant treatment.

Hopefully, people will be able to see how the work that scientists are doing to engineer adult cells for the treatment of diseases is different from what Dr. Jiankui did.  One of the most important things we need to get across is that there is nothing wrong with CRISPR or gene editing in general.  Gene editing is a powerful research tool with lots of benefits not only for general research but also for medical treatment.  Scientific techniques are not good or bad by themselves; they are only good or bad in how people use them.  After all, I bet Victoria Gray likes CRISPR.

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The Teaching Cyborg

Gene Editing in Humans Part Two

“The power to control our species’ genetic future is awesome and terrifying. Deciding how to handle it may be the biggest challenge we have ever faced.”
Jennifer A. Doudna

A year ago, He Jiankui announced that he had used CRISPR to create two gene engineered baby girls.  Since the initial announcement, there has been little new information released.  The government terminated Dr. Jiankui’s lab and research activities. “China’s Vice-Minister of Science and Technology Xu Nanping quickly shut down Dr He’s lab, ordering a full investigation and flagging some form of punishment for the researchers.”  It is also not clear where Dr. Jiankui is located “Hong Kong media reported that the university president, Chen Shiyi, personally flew to Hong Kong to collect and escort Dr He back to Shenzhen, where he was put “under house arrest”. The university denied Dr He was detained, telling the South China Morning Post “nobody’s information is accurate” on Dr He’s whereabouts, but refused to provide any details.

For about a year, this was the state of the information about the first two genetically engineered human beings.  Then early this month (Dec 2019), MIT Technology Review published a series of articles about Dr. Jiankui’s research.  It seems that He Jiankui wrote a 4699-word article titled “Birth of Twins After Genome Editing for HIV Resistance,” while the paper remains unpublished Dr. Jiankui submitted it to Nature and JAMA the Journal of the American Medical Association (China’s CRISPR babies: Read exclusive excerpts from the unseen original research.) Dr. Jiankui’s unpublished work answer several questions that were left unanswered last year.  However, the answers are perhaps more troubling than the speculation.

To understand what Dr. Jiankui was trying to accomplish, we need a little bit of history. Dr. Jiankui calms that he was trying to engineer humans to be resistant to HIV. The HIV-1 virus infects CD4 immune cells.  Over time an individual infected with HIV reaches a point where they cannot produce enough CD4 cells to mount a viable immune response. Leading to the collapse of the immune system and often death by disease.  Around 1996 a naturally occurring mutation in the CCR5 gene was discovered that rendered individuals resistant or possibly immune to infection by the HIV-1 virus.  The CCD5 mutation is a deletion of 32 base pairs (called Δ32) in the coding sequence of the CCR5 gene.  (Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection.)

The Δ32 mutation makes it so that the HIV-1 virus can’t bind to the CCR5 protein.  Since the HIV-1 virus uses the CCR5 receptor to enter cells, this mutation renders cells resistant or immune to infection by HIV-1.  According to his paper, Dr. Jiankui used the CRISPR technology to engineer the CCR5-Δ32 mutation into the in-vitro fertilized embryos of a couple where the husband was HIV positive, and the wife was HIV negative. The genetic change, in turn, would confer immunity to the children born from these embryos.

In the abstract, Dr. Jiankui says they were successful in editing the CCR5 gene.  “Genomic sequencing during pre-implantation genetic testing and after birth confirmed that the twins’ CCR5 genes were edited successfully and are thus expected to confer either complete or partial HIV resistance.” (China’s CRISPR babies: Read exclusive excerpts from the unseen original research) However, the actual data in the paper shows that one of the embryos has a frameshift mutation in the CCR5 gene, while the second embryo has a 15 bp delegation.  While both mutations cause changes in the CCR5 protein, they do not create the same disruption as the CCR5-Δ32 mutation.  It is not clear that these mutations will confer immunity to HIV since not every single mutation in CCR5 confers HIV immunity.  Beyond the question of the effectiveness of the created mutations, new research suggests that being homozygous for the CCR5-Δ32 mutation leads to a decrees in life expectancy (CCR5-∆32 is deleterious in the homozygous state in humans.)  Additionally, it appears that the cells in the embryos may not have all changed to the same extent leading to mosaics.

In addition to the potentially harmful nature of CCR5 mutations, there is a question about the type of genetic engineering.  If you are going to induce a mutation in a gene because of an observed effect, you need to create the same mutation that caused the original effect, not a similar mutation.  The reason is twofold one if you create a new mutation, you don’t know that the new mutation will have the same effect as the old one.  Two of the new mutation could cause a new and unintended consequence that the original mutation did not have.

Now at a first pass, Dr. Jiankui’s motives sound reasonable and altruistic.  He is trying to help a couple that is HIV positive have children.  Dr. Jiankui even states in his abstract, “Millions of children are born annually with inherited genetic diseases or infectious diseases acquired from parents.”  (China’s CRISPR babies: Read exclusive excerpts from the unseen original research) As stated by Rita Vassena, scientific director of the Eugin Group, there are well-established techniques to prevent transmission of HIV from parent to offspring. 

“It is worth remembering that HIV infection is not passed on through generations like a genetic disease; the embryo needs to “catch” the infection. For this reason, preventive measures such as controlling the viral load of the patient with appropriate drugs, and careful handling of the gametes during IVF, can avoid contagion very efficiently.” (China’s CRISPR babies: Read exclusive excerpts from the unseen original research

From a medical point of view, it is rarely if ever considered acceptable to use an experimental and potentially dangers technique when effective options already exist.

Beyond the question of whether the technology was ready, Dr. Jianjui’s foray into genetic engineering brings into sharp focus a question about the utilization of genetic engineering.  Dr. Jianhui attempted to create a new biological function in the twins.  He tried to engineer viral resistance.  What makes this especially troubling is that while we know that CCR5-Δ32 confers resistance to HIV-1 research into the normal biological functions of CCR5 is still ongoing.  The work showing that being homozygous for the CCR5-Δ32 can be harmful to the life span was published this year (2019). Instead of trying to create something “new,” why didn’t Dr. Jianjui try and fix a “broken” gene.

If Dr. Jianjui had at least tried to use genetic engineering to reverse a disease-causing mutation to the normal function, he would not have had to deal with the potential conquests of changing a gene function he would have restored it to normal function.  While this article should make it clear that gene-editing technology is not yet specific enough for reproductive genetic engineering, at the rate the technology is improving, it will not be long before we the technology can make specific changes in an embryo without producing additional defects.

A companion article also from the MIT Technology Review Opinion: We need to know what happened to CRISPR twins Lulu and Nana States that Dr. Jianjui’s papers need to be made public.  Specifically, Dr. Kiran Musunuru says, “Why must the information be public? It’s because He’s work reveals serious, unresolved safety concerns. It’s not clear that any effort to directly edit human embryos, even if done ethically and with full social approval, can reliably avoid these problems.”  While I think Dr. Musunuru’s interpretation is a little extreme.  I don’t believe Dr. Jianjui had a good enough grasp of what he was trying to do to use his research as a cornerstone of the technology limits.  After all, most of the information uncovered in his unpublished work is in aliment with the concerns and beliefs put forward by the scientist when human engineering was first made public.  I do agree that we need to discuss the uses and potentials of genetic engineering.

However, for people to have discussions about the ethics of genetic engineering, people need to understand the basics of genetics and genetic engineering.  Humans have been using genetic engineering since we planted our first crops and domesticated the first animals.  Our faithful companion, the dog, is the product of thousands of years of genetic engineering.  We are entering a point when we can change our ecosystem and ourselves at a rate faster than ever before. However, how much does the general public know about genetics?  Can we make a legitimate decision about genetic engineering if we don’t even understand the basics of what is going on?

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The Teaching Cyborg

Is it Dedication or Delusion?

“Delusion is the seed of dreams.”
Lailah Gifty Akita

Educational reform is a never-ending process, which is, in many ways, good.  The purpose of educational institutions is to provide the best education possible.  The individual teacher learns from experience and improves over time.  Research into learning and cognition lead to better understandings of how people learn and therefor better ways to teach.

However, even with our continually improving knowledge, changes in education seem painfully slow or to not occur at all.  A consistent problem is classroom size.  While just about anyone that has studied education will agree that the best way to teach someone is with a dedicated teacher in a one on one environment (feel free to disagree I would love to hear your reasons). However, in a society that wants education especially higher education available to everyone one on one education is not possible.

Don’t believe me look at the numbers.  According to the US census bureau, there are 76.4 million students in school K through University.  That means we would need 76.4 million teachers if we paid them an average living wage including overhead each teacher would make $41,923 – $46,953 (still a little low if you ask me)  this works out to 3.2 – 3.5 trillion dollars or 17-19% of the US Gross National Product.  As a comparison, the budget for the US national government was 21% of the GDP in 2015.  Also, 76.4 million students are 24.7% of the US population, three and older, if we also had 24.7% of the US population working as teachers, then almost half of the US population would be students or teachers. Remember we would still need all the support staff, and these are with current numbers, not what we would need for everyone eligible for school.

I don’t think any country can afford to devote that much of their population and resources to one thing and survive.  As someone that loves education, I would love it if some economist out there proves me wrong.  So, class size is a compromise between what we can afford to do and the best environment for our students.

However, outside of issues that are constrained by shall we call it a reality.  We have all seen programs and projects that we think can help students get canceled.  We have all seen programs developed by grants get canceled the second the grant ends.  The loss of these programs is not only that future students will not benefit, but also the loss of resources, including time, commitment, and motivation of staff.

I have been asked after several of my programs have been canceled “how many times are you going to keep building programs that just get canceled?” It’s an interesting question and one that is not easy to answer.  I was at the University of Colorado Boulder when Carl Wieman won the 2001 Noble prize for Physics.  After winning the Nobel prize, Wieman went on to advocate for the improvement of science education.  To the extent that he was appointed the White House’s Office of Science and Technology Policy Associate Director of Science in 2010.  In 2013 I remembered reading an article Crusader for Better Science Teaching Finds Colleges Slow to Change that was about Dr. Weiman and his frustrations with the slow changes in higher education “… Mr. Wieman is out of the White House. Frustrated by university lobbying and distracted by a diagnosis of multiple myeloma, an aggressive cancer of the circulatory system, he resigned last summer. … “I’m not sure what I can do beyond what I’ve already done,” Mr. Wieman says.”

You can’t help but think if someone with the prestige and influence of Carl Weiman can’t encourage change what hope does anyone else have.  The truth of the matter is that how much someone can take and when they have had enough is a personal question.  When thinking about how much is enough, I can’t help but think of a humorous little fable Nasreddin and the Sultan’s Horse.  I have encountered versions of this fable many times.  I think the first time was in the science fiction book The Mote in God’s Eye by Larry Niven and Jerry Pournelle.

Nasreddin and the Sultan’s Horse

One day, while Nasreddin was visiting the capital city, the Sultan took offense to a joke that was made at his expense. He had Nasreddin immediately arrested and imprisoned; accusing him of heresy and sedition. Nasreddin apologized to the Sultan for his joke and begged for his life; but the Sultan remained obstinate, and in his anger, sentenced Nasreddin to be beheaded the following day. When Nasreddin was brought out the next morning, he addressed the Sultan, saying “Oh Sultan, live forever! You know me to be a skilled teacher, the greatest in your kingdom. If you will but delay my sentence for one year, I will teach your favorite horse to sing.”

The Sultan did not believe that such a thing was possible, but his anger had cooled, and he was amused by the audacity of Nasreddin’s claim. “Very well,” replied the Sultan, “you will have a year. But if by the end of that year you have not taught my favorite horse to sing, then you will wish you had been beheaded today.”

That evening, Nasreddin’s friends could visit him in prison and found him in unexpected good spirits. “How can you be so happy?” they asked. “Do you really believe that you can teach the Sultan’s horse to sing?” “Of course not,” replied Nasreddin, “but I now have a year which I did not have yesterday, and much can happen in that time. The Sultan may come to repent of his anger and release me. He may die in battle or of illness, and it is traditional for a successor to pardon all prisoners upon taking office. He may be overthrown by another faction, and again, it is traditional for prisoners to be released at such a time. Or the horse may die, in which case the Sultan will be obliged to release me.”

“Finally,” said Nasreddin, “even if none of those things come to pass, perhaps the horse can sing.”

In 2017 I read an article from Inside Higher Ed Smarter Approach to Teaching Science.  The article talks about a book (Improving How Universities Teach Science: Lessons from the Science Education Initiative) written by Carl Weiman that documents the research and methods to improve science teaching in higher education.  It seems that Dr. Weiman did not give up after all, and he is back and still pushing.  Perhaps the truth is that people that try and change the monolith must be a little bit crazy if crazy is doing the same thing repeatedly and expecting a different outcome. Then again, maybe the horse will learn to sing.

Thanks for Listing to My Musings
The Teaching Cyborg

1, 2, 3, 4, 5, and 6? Extinctions

“Extinction is the rule. Survival is the exception.”
Carl Sagan

An article in Scientific America asked an interesting question, Why Don’t We Hear about More Species Going Extinct? There have been a lot of stories about the planet being in the middle of the 6th mass extinction.  Reports are saying that the rate of extinction is as much a 1000 times normal.  If these articles are correct shouldn’t we see articles in the news about species going extinct?  However, I wonder if people even understand the context of mass extinctions?  If asked, what is a mass extinction, could you answer? 

To understand what a mass extinction is, we need to understand life on earth and the fossil record.  All five existing mass extinctions are in the fossil record.  The first life that appeared were microbes around 3.7 billion years ago.  They lived in a world that was quite different from present-day earth.  The atmosphere was almost devoid of O2 (molecular oxygen) and high in things like methane.  Molecular oxygen is highly reactive and will spontaneously react with any oxidizable compounds present.  The early earth was full of oxidizable compounds, any molecular oxygen that did appear was almost instantly removed by chemical reaction.

About 1.3 billion years later the first cyanobacteria evolved, these were the first photo-synthesizers. Over possibly hundreds of millions of years molecular oxygen produced by the cyanobacteria reacted with compounds in the environment until all the oxidizable compounds were used up.  A great example of this is banded iron deposits.  Only when molecular oxygen reacted with all the oxidizable compounds could molecular oxygen begin to accumulate in the environment. 

After another 1.7 billion years the first multicellular organisms, sponges appeared in the fossil record.  Around 65 million years later a group of multicellular organisms called the Ediacaran Biota joined the sponges on the seafloor.  Most of these organisms disappeared around 541 million years ago.  However, the loss of the Ediacaran Biota is not one of the five mass extinction events.  How much of an evolutionary impact the Ediacaran Biota had on modern multicellular organisms is still an open question.  Most of the Ediacaran Biota had body planes quite different from modern organisms.

The next period is especially important; it started about 541 million years ago and lasted for about 56 million years.  The period is known as the Cambrian.  This period is referred to as the Cambrian explosion because all existing types (phyla) of organisms we see in modern life emerged during this period. The Cambrian explosion is also essential because the diverse number and types of organisms that evolved during the Cambrian explosion form the backdrop for mass extinctions.

The first mass extinction occurred 444 million years ago at the end of the Ordovician period.  During this extinction event, 86% of all species disappeared from the fossil record over about 4.4 million years. Global recovery after the extinction event took about 20 Million years

The Second mass extinction occurred at the end of the late Devonian Period.  The Devonian extinction is the extinction that eliminated the Trilobites.  During this extinction event, 75% of all species disappeared from the fossil record over as much as 25 million years

The third and largest mass extinction occurred at the end of the Permian period 251 million years ago.  During this mass extinction, 96% of all species disappeared from the fossil record over 15 million years.  Research suggests that the Permian mass extinction took 30 million years for full global recovery.

The fourth mass extinction occurred 200 million years ago at the end of the Triassic period.  During this mass extinction, 80% of all species disappeared from the fossil record. The Triassic mass extinction appears to have occurred over an incredibly short period, less than 5000 years.

The fifth mass extinction occurred at the end of the Cretaceous period 66 million years ago.  This extinction is by far the most famous of the mass extinctions because it is the meteor strike that killed the dinosaurs.  During this extinction, 76% of all the spices disappeared from the fossil record.  Research suggests this mass extinction only took 32,000 years.

Now that we have looked at mass extinctions what about regular extinctions.  Normal or background extinction rate is the number of extinctions per million species per year (E/MSY).  Current estimates put the background extinction rate at 0.1 E/MSY.  If the the current extinction rate is 1000 times the background extinction rate, then currently the extinction rate is 100 E/MSY.

The current estimate for the total number of species is 8.9 million.  That means that 890 species are going extinct every year or 2.5 species a day.  So why don’t we hear more about spices going extinct if the extinction rate is that high?  First, the current catalog of identified species is 1.9 million, which means there are currently 7 million species (79%) that are undescribed.  That means 700 of the 890 extinctions a year would be in species that scientists haven’t identified.

The second problem is that even with identified species, it is often difficult to know if a species has gone extinct.  The International Union for Conservation of Nature (IUCN) maintains the Red List of critically endangered species.  One of the categories is Possibly Extinct (PE) based on the last time anyone saw an organism.  For example, no one has seen the San Quintin Kangaroo Rat in 33 years, no one has seen the Yangtze River Dolphin in 17 years, and no one has seen the Dwarf Hutia in 82 years.  It is likely that these three spices, along with several others, are extinct.

However, not being seen is not good enough to classify a species extinct.  After all, the Coelacanth was thought to be extinct for 65 million years until a fisherman caught one in 1938.  For a species to be declared extinct, a thorough and focused search must be made for the organism to declare it extinct.  These types of searches require time, personnel, and money.  Therefore, searches don’t often happen.  So with the exceptions of particular cases, like Martha the last Carrier pigeon who died on September 1, 1914, most species go extinct with a whimper, not a bang.

We don’t hear more about species going extinct because even knowing extinctions are occurring, in many cases, we don’t know about them.   Returning to the question of what is a mass extinction, and could there be a 6th happening?

Use the five existing mass extinctions as examples a simple definition of a mass extinction is an event where 75% or more of the existing species become extinct within a short (less than 30 million years) time.  Using the current estimated number of spices, and the current estimated rate of extinction we can calculate how long it will take to reach the 75% mark the answer is 7500 years. Since 7500 years is less than 30 million years, we could be on course for a 6th mass extinction.  However, as Doug Erwin says we are not in the middle of the 6th mass extinction.  If we were in the middle of a mass extinction like Dr. Erwin said cascade failures would already have started in the ecosystem and there would be anything we could do.  However, that is good news we still have time to do something.

What we need is an accurate count of extinct species.  So, do you have a class that could do fieldwork?  There is probably a critically endangered species near you.  Maybe you will even be lucky, and you will find the species then you can help with a plan to save it.

Thanks for Listening to My Musings
The Teaching Cyborg

If We Want to Discuss Scientific Ethics, We Need to Teach Scientific Literacy

Science literacy is the artery through which the solutions of tomorrow’s problems flow.”
Neil deGrasse Tyson

Late last year a Chinese scientist He Jiankui announced that his team had created two genetically engineered human embryos that lead to the birth of two female siblings.  I wrote an article about why this shouldn’t have surprised anyone (It Might Have Happened, We Don’t Know for Sure, But Now We Freak.) While there may still be some questions, all the technology needed currently exists.

In June 2019 Russian scientist Denis Rebrikov announced that he plans to seek approval from several government agencies to perform a similar experiment to He Jiankui. It is not currently clear that human genetic engineering is legal under Russian law, or that Dr. Rebrikov will receive approval for his trial.

Beyond genetically engineering humans a few days ago (Aug 3, 2019) a report came out about the creation of a Human-Monkey chimera First Human–Monkey Chimeras Developed in China. Professor Juan Carlos Izpisúa Belmonte’s group of the Salk institute conducted the experimented in China.  According to the report, the scientists chose to perform the research in China to avoid legal issues. The same group produced a human-pig chimera in 2017.

On top of questions concerning human experimentation, there are questions about Genetically Modified Organisms (GMOs).  Just like debates about human genetic engineering, the discussions about GMOs are occurring after the fact.  Today more then 90% of the Hawaiian Papaya crop is Genetically modified (How GMO Technology Saved the Papaya).  Other conventional crops like corn, soybeans, and canola oil are also mostly GMO.

I could continue listing procedures that are emerging that have or will have ethical debates associated with them.  However, if we are going to have meaningful discussions, it is essential that individuals have a basic scientific understanding.  Specifically, what are the techniques scientists use and why were they chosen.  What is genetic engineering?  What is a Chimera?  What are stem cells?  Why are we interested in these techniques?  Why should we use them? 

Let’s start with the basics according to Merriam Webster

  • Genetic engineering: the group of applied techniques of genetics and biotechnology used to cut up and join together genetic material and especially DNA from one or more species of organism and to introduce the result into an organism in order to change one or more of its characteristics
  • Chimera: an individual, organ, or part consisting of tissues of diverse genetic constitution
  • Stem cells: an unspecialized cell that gives rise to differentiated cells

While a few of these definitions could lead to additional questions, what does “diverse genetic constitution” mean, I can live with them.  These definitions would be a good starting point for discussions in class.  However, a lot of today’s society is like to go to Wikipedia instead of the dictionary.

  • Genetic engineering: Genetic engineering, also called genetic modification or genetic manipulation, is the direct manipulation of an organism’s genes using biotechnology.
  • Chimera: A genetic chimerism or chimera (/kaɪˈmɪərə/ ky-MEER-ə or /kɪˈmɪərə/ kə-MEER-ə, also chimera (chimæra) is a single organism composed of cells with distinct genotypes.
  • Stem cells: Stem cells are cells that can differentiate into other types of cells, and can also divide in self-renewal to produce more of the same type of stem cells.

Fortunately for society, many of these definitions are excellent; in fact, the Wikipedia definition of Genetic Engineering and Stem cells is probably better than Merriam Webster’s definition.

So that means that GMOs are the product of Genetic Engineering. So why would you want to create GMOs?  There are lots of reasons let’s talk about Golden rice.  Golden rice is a GMO designed to combat vitamin A deficiency.  Due to starch content, white rice is a good source of calories. However, rice lacks several essential nutrients (including vitamin A).

To combat Vitamin A deficiency, scientists engineered rice to produce β-carotene, which the human body turns into vitamin A.  Scientists created Golden rice by the insertion of two genes into the rice genome.  The final product is rice, that is a golden color and provides β-carotene.  So, in the case of golden rice, the reason for genetic engineering was to combat malnutrition. Other researchers are trying to create crops that need less fertilizer or pesticides, that have better yields, or to do less damage to the soil.

There are people that no matter what the goal is will say GMOs should be outlawed.  The question, of course, is why? After all, we have been modifying our food for thousands of years.  Let’s talk about Cauliflower.  The many types of cabbage, broccoli, kale, kohlrabi, and cauliflower are all descended from the same plant. Brassica oleracea also called wild cabbage (The extraordinary diversity of Brassica oleracea).

Brassica oleracea (wild cabbage) photo by Kurt Kulac,. Licensed under the Creative Commons Attribution-Share Alike 2.5 Generic license.
Brassica oleracea (wild cabbage) photo by Kurt Kulac,. Licensed under the Creative Commons Attribution-Share Alike 2.5 Generic license.

Over thousands of years farmers selected for traits they found desirable, leading to all the variants, many of which don’t even look like the same plant like cauliflower.

A cauliflower plant photographed by Bloemkool. Licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.
A cauliflower plant photographed by Bloemkool. Licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.

Research into Arabidopsis thaliana flower development by scientists using a mutagen (a chemical compound that creates changes in DNA) to create mutations.  One of these mutations produced plants that looked like cauliflower (Molecular basis of the cauliflower phenotype in Arabidopsis).  Additional research showed that the gene muted in Arabidopsis to produce the cauliflower phenotype was the same naturally occurring mutation in Brassica oleracea that was selected to produce cauliflower.

The research into plant development means that I could reproduce cauliflower in three different ways.  One, I could selectively breed Brassica oleracea to produce cauliflower.  Two, I could create mutations in Brassica oleracea using chemical mutagens and select for cauliflower.  Three, since we know the gene, I could use genetic engineering to create cauliflower from Brassica oleracea.  Most importantly done correctly, I could produce cauliflower using all three of these methods, and genetically, they would be identical.  However, even though there would be no difference between the three varieties, people would insist that the GMO cauliflower caused all kinds of problems, why?

While GMOs are already out in the wild and because of the spread of pollen, it is unlikely that society will ever put GMOs back in the box.  With several of the recent occurrences, it might also be too late for human genetic engineering, human GMOs.  Now let’s talk about Chimera’s. 

One of the primary goals for human-monkey or human-pig chimeras is the production of organs for transplant.  A common statistic is that 20 people die every day in the US waiting for a transplant. In the case of organ transplants, individuals would donate cells that scientists combine with an early pig embryo. The human cells would then give rise to the lungs, which doctors would transplant.  Currently, scientists have not produced chimeras with enough human cells to create organs that are viable for transplant.  However, it is only a matter of time until this becomes possible.  Will people wait until the first transplant occurs to talk about chimeras?

However, just as significant as the question, “will we discuss something before it happens?” Is the question of whether we are doing enough to teach science so the general society can adequately discuss the issues?  How important do you think science classes for nonmajors are?  Nonmajors class might make all the difference to the future of scientific research and medical improvements.

Thanks for Listing to My Musings
The Teaching Cyborg

Increasing STEM Graduation Numbers

“You cannot teach a man anything; you can only help him discover it in himself.”
Galileo

For decades the United States government has told us that we need to turn out more STEM graduates.  I remember hearing in my youth the government talk about needing more science graduates; Rita Colwell had not yet coined the term STEM.

On December 18, 2012, President Barack Obama announced a plan to add 1 million more STEM graduates over the next decade (Obama White House.)  In 2018 the Committee on STEM education in their report CHARTING A COURSE FOR SUCCESS: AMERICA’S STRATEGY FOR STEM EDUCATION said, “Since 2000, the number of degrees awarded in STEM fields has increased, but labor shortages persist in certain fields requiring STEM degrees.”

Researchers have proposed that one of the biggest reasons for the lack of STEM graduates is the lack of Primary and High School STEM teachers.  Especially high school physics teachers, according to a 2011 report by the US Department of Education only about 46.7% of all high school physics class are taught by a teacher with a degree in the subject.  Furthermore, according to a report from the U.S. Department of Education Office for Civil Rights, only 63% of US high schools offer physics.

Decades into the problem, what do we do to increase the number of people graduating with STEM degrees?  Most of the programs focus on expanding the pipeline getting more people interested in STEM careers at an earlier age.  While these types of programs are essential and vital, especially in the cases of underrepresented groups, I wonder if there might be a better way to increases STEM graduates.

Another way to increase graduation rates would be to increase STEM retention.  Even all these years later, I still remember my first core biology course as an undergraduate.  The professor taught the course in the largest lecture hall on campus; there were over 500 students in that class.  By the end of the core biology sequence, there were less than 250 students left.

According to the National Center for Educational Statistics report STEM in Postsecondary Education: Entrance, Attrition, and Course taking Among 2003−04 Beginning Postsecondary Students, 27.8% of the 2003-04 starting class registered as STEM majors.  According to the same report, 51.7% of the students that started in STEM degrees graduated with a STEM degree. Also, according to the National Center for Educational Statistics, the total student enrolment for fall 2003 was 16,911,481 (https://nces.ed.gov/programs/digest/d13/tables/dt13_303.10.asp retrieved July 27, 20019.)

Using these numbers, the 2003-04 incoming class had 4.7 million registered STEM majors.  By the 5-year graduation mark, the 2003-04 starting class had graduated 2.4 million students with STEM degrees.  Which means the 2003-04 class had lost 2.3 million STEM majors.  If the 2003-04 graduating class had graduated 73% instead of 51.7%, there would have been 1 million more graduating STEM majors.  The same number that Obama set but in half the time and without any changes to the incoming pipeline.

Beyond just increasing the overall number of STEM graduates, increased retention can help in other areas.  For example, from the 2003-04 incoming class, 14.2% of the female students that started as STEM majors left postsecondary education while 32.4% left STEM for other majors. (STEM Attrition: College Students’ Paths Into and Out of STEM Fields Statistical Analysis Report)  Conversely, 23.1% of the Hispanic students that were STEM majors left postsecondary education entirely while 26.4% left STEM majors for other fields. We see similar trends in Black students, 29.3% left higher education without a degree, and 36% left STEM for other majors.  The numbers were lower for Asian students, 9.8% left without a degree, while 22.6% changed to other majors. (STEM Attrition: College Students’ Paths Into and Out of STEM Fields Statistical Analysis Report).

Again, if we could increase the retention rate of these students by 50%, we would add a lot of Female, Hispanic, Black, and Asian STEM majors. The most significant advantage of increasing retention rates to increase the number of STEM graduates is we are already dealing with a group that has an interest in STEM.  Additionally, working on increasing retention forces us to decide if the educational goal for undergraduate students is teaching STEM or sorting STEM students.  After all, it is about time that we remember, not all STEM major wants to get a Ph.D. and become a professor.  At the undergraduate level, we should be teaching STEM students so that they can use their skills to pursue their paths. Thanks for

Listing to My Musings
The Teaching Cyborg