Thursday, December 6, 2018

He Jiankui Found a Week Later Holed Up Playing Red Dead Redemption 2 (Parody)

He Jiankui made international headlines in November for using CRISPR-Cas9 to edit the genes of two human embryos without approval. He was swiftly made an international pariah by the scientific community due to the highly unethical process by which he conducted his experiments, with everyone from Francis Collins to Jennifer Doudna throwing shade his way.

Things took a sinister turn last Wednesday (11/28) when He went missing, with no clear explanation for how or why (see this article for details). A spokeswoman from Southern University in China stated "right now nobody's information is accurate, only the official channels are," a curious thing to say when the official channels have been remarkably silent. The Chinese government has shut down He's lab and firmly denounced He's actions, but has not commented on He's disappearance.

So what happened to He Jiankui? Did he get lost while out on a stroll through the neighborhood? Did he go into hiding to avoid further public criticism after being ridiculed for what he considered to be a historic step forward for humanity? Did the Chinese government "disappear" him because he made them look bad? Is he being secretly detained without access to legal council for a potentially indefinite amount of time? Did he retreat to his secret lab in the South China Sea to continue his experiments where ethics boards and government regulations can't reach him? If so will he reemerge in 30 years with an army of genetically modified CRISPR super babies to retake the mainland?

All of these questions were put to rest earlier today when a student from his lab snuck into his house using a spare key to ask whether or not He had submitted that letter of recommendation she had been asking about.

She was amazed to find him safe and content on his sofa shooting deputies and robbing banks in Red Dead Redemption 2. Apparently, He had completely forgotten about the international uproar surrounding his actions and was now focused primarily on hunting legendary animals and accumulating a hoard of cash. "I like the way rules and regulations don't apply in the world of Read Dead," He stated while kicking a woman off a cliff. "You can shoot people, steal stuff, do whatever you want, and there aren't any real consequences. The free-form gameplay and open environment really lets you be the person you want to be, let's you do the things you want to do."

For more updates on He Jiankui you can watch him stream live on Twitch, his new primary source of income. His username is @bethegodyouweremeanttobe.

 *This was my first parody article (I'll always point out if what I'm writing is parody). I very much hope the scientific community can resolve the ethical and technical maelstroms surrounding CRISPR and we get to a point where we can use it for good--under the guidance and direction of the appropriate entities--and applied to the appropriate diseases. I also hope He Jiankui is alright, wherever he actually is. At there very least, we need an answer from the Chinese government on what happened, and we need to hold the Chinese government accountable if they met one unethical action with another.



Monday, September 10, 2018

MD/PhD Research Experience Essay Example

Application for MD/PhD programs requires three essays:
  1. Personal Statement
  2. MD/PhD Essay (a statement of interest specifically for both MD and PhD degrees)
  3. Research Experience Essay (a detailed description of your research experiences)
I published my MD/PhD Essay as an example for students back in 2014 (link above). Hopefully my research essay will also be a helpful example.

My MD/PhD Research Essay

Prompt: Describe your significant research experiences. In your statement, specify your research supervisor's name and affiliation, the duration of the experience, the nature of the problem studied, and your contributions to the project.

1) Toxicology, Ichthyology, and Marine Ecology Lab
Dr. Sandra Diamond (Ph.D., Zoology, North Carolina State University), Assistant Professor, Texas Tech University
January 2011-Present
1a) Antibiotic Toxicology Project (January 2011-May 2012)
My research with Dr. Diamond began with the examination of an antibiotic, Triclosan, that is included in many personal care products. After use, Triclosan is carried through drains to wastewater treatment plants. While some of the Triclosan is purged from waterways, a significant amount escapes and reaches the oceans. There, it is incorporated into the fatty tissue of benthic organisms, where it interferes with calcium signaling. The widespread distribution of Triclosan is beginning to cause humans to acquire significant levels of Triclosan, especially in breast milk. This could generate antibiotic-resistant bacteria, and may even impede calcium signaling in humans. Our goal is to understand the potential dangers of Triclosan in the environment.
I contributed to this project by working closely alongside a graduate student and constructing a literature matrix on how Triclosan behaves in the ocean. I participated in laboratory experiments, collected data, maintained the laboratory, and helped proofread material for presentations.
For my work, I was acknowledged in "The Effects of Triclosan on Reflex Responses and Anti-Predator Behavior in an Estuarine Fish" (Tiffany L. Hopper-Hedrick and Sandra L. Diamond), a poster that my group presented at the Ecological Society of America.
1b) TTU Shark Team (May 2012-December 2012)
Upon completion of the toxicology project, Dr. Diamond hired me onto the TTU Shark Team, a group seeking to establish multi-national management of shark fisheries in the Gulf of Mexico through a deeper understanding of shark ecology. Historically, the oceans have been overexploited due to advances in technology and competition for resources. Because sharks have long generation times, they are particularly vulnerable. We use geographic information systems and statistical analyses to map out seasonal distributions for fourteen species of sharks.
In this group I contributed to the construction of a literature matrix containing over 800 papers to communicate large-scale trends, such as seasonal distributions. This experience has developed my critical reading skills, increased my general understanding of scientific thought, and prepared me to design an experiment of my own.
1c) TTU/Howard Hughes Medical Institute Affiliated Project (May 2012-Present)
After earning designation as a TTU/Howard Hughes Medical Institute Undergraduate Research Scholar in May of 2012, Dr. Diamond gave me the scientific freedom to design and carry out a research project.
The concentration of carbon dioxide in our atmosphere is increasing, causing the pH of the oceans to lower significantly. In addition, ocean fertilization (the mass addition of nitrogen and phosphorus) is causing algal blooms. Because algae use up oxygen, the dramatic increase in algal populations has resulted in the creation of 'dead zones' in which there is little or no oxygen. My research examines the synergistic effects of acidification and hypoxia on Atlantic Croaker.
I am responsible for designing experiments, writing protocols for acceptance by our Animal Care and Use Committee, collecting data, making decisions concerning our budget, communicating with companies to purchase scientific equipment, and writing a technical paper. Five months ago, I was given the responsibility of organizing and training five undergraduates in our lab to maintain our artificial ocean system while Dr. Diamond was in Australia for two semesters. In addition, an undergraduate researcher worked on a sub-assignment under my project.
I have presented my work in this lab at four conferences: Texas Tech University Health Sciences Center Student Research Week, TTU/Howard Hughes Medical Institute Best and the Brightest: Research Forum, The Texas Chapter of the American Fisheries Society, and Texas Tech University Undergraduate Research Conference. Abstracts for this work have been accepted at the Arkansas Chapter of the American Fisheries Society and the 2013 TTU/Howard Hughes Medical Institute Undergraduate Research Forum.
I was also part of a panel of researchers from TTU for Earth Day at North Ridge Elementary School. At this event, I delivered a presentation on Marine Biology and Environmental Sustainability with an emphasis on mantis shrimp and sharks.

2) Plant Evolution and Ecology Lab
Dr. Dylan Schwilk (Ph.D., Ecology and Evolution, Stanford University), Assistant Professor, Texas Tech University
October 2012-Present
2a) TTU/Howard Hughes Medical Institute Affiliated Project (October 2012-Present)
In Dr. Schwilk’s lab, we are pursuing an understanding of tree ecology in the mountain ranges of Texas. The water transporting vessels (xylem) of trees become clogged, much like arteries in humans, in a process known as drought-induced embolism. Although it is impossible for negative pressures to exist in gaseous systems, this is not the case with liquids. Trees rely on extreme negative tension to pull water to heights much greater than those allowed by adhesion, cohesion, or atmospheric pressure. When trees experience drought conditions, the strength of these tensions increases as the amount of water available to them decreases. This makes the pressure within the xylem so low that water starts to boil, and bubbles form within vessels. Once a certain percentage of the xylem within a branch becomes embolized, it is sacrificed by the tree. My project examines the point at which branches are sacrificed in four oak species.
My reasons for joining Dr. Schwilk’s lab are unique. Normally, TTU/HHMI Scholars work in a single lab due to the expected levels of involvement. However, in October of 2012, one of my fellow scholars, Chris, passed away in an automobile accident. Because the TTU/HHMI Scholars are a tight-knit family, I decided to inherit his project and finish it for him. I invited every TTU/HHMI Scholar to participate in completing his project to help us heal as an organization.
My responsibilities in Dr. Schwilk’s lab include writing, modifying, and developing the protocol for an experiment, training undergraduate researchers and delegating scientific tasks, participating in expeditions to the Davis, Guadalupe, and Chisos Mountains, carrying out laboratory experiments, and recruiting new laboratory members.
I led one trip to Davis Mountains with a single non-scientist assistant to gather data.
An abstract for this work has been accepted for the 2013 TTU/Howard Hughes Medical Institute Undergraduate Research Forum, where I will present our findings in honor of Chris’s memory.
For simultaneously working full-time in the Diamond and Schwilk labs, successfully lobbying for Texas Tech University to continue its support of TTU/HHMI, and organizing and training groups of scholars to participate in Chris’ project, I received the Dr. Richard L. Blanton Endowment for Undergraduate Research.

3) Honors Thesis in Physics and Biology
Dr. Micah Green (Ph.D., Chemical Engineering, Massachusetts Institute of Technology), Assistant Professor, Texas Tech University
January 2012-Present
3a) Honors Thesis as part of the TTU Honors College
I received approval in January of 2012 to conduct an Honors Thesis outside of my major on the fine-tuning of four cosmic parameters in phase space. Normally, students are encouraged to pursue topics related to their undergraduate major when conducting an Honors Thesis. However, I was allowed to proceed with a physics-based inquiry, since I had gained competency in physics and cosmology as a result of personal study.
Over the past hundred years, physicists and cosmologists have started to notice that if certain fundamental characteristics of our universe had been anything other than what they are, the evolution of life in our universe would have been impossible. An example of one of these characteristics, called “parameters”, is the gravitational constant. If the force of gravity had been stronger during the big bang, the exploding matter would have re-condensed into a black hole. Alternatively, if gravity had been weaker during the big bang, there would not have been enough attraction between particles for stars to form, resulting in a universe comprised almost entirely of hydrogen and helium. In either case, the evolution of life in our universe would have been impossible. The general consensus of the scientific community at this point is that many parameters are finely tuned, meaning that miniscule variations in their values would render the universe lifeless.
My Honors Thesis is a review of the current scholarly conversation on the fine tuning of the universe. My primary insight concerns the target of fine tuning. Historically, physicists assumed that the universe needed to be fine-tuned for our form of carbon-based life specifically. As an evolutionary biologist, I know that this is not the case. A universe only needs to maintain a stable environment, contain the essential building blocks for complex molecules, and be expansive enough for origin events to be probable. Once an origin event takes place, natural selection could cause those collections of molecules to evolve in any number of directions. Dr. Green and I conclude that our four target parameters display fine tuning, but to a much lesser degree than has traditionally been accepted.
Because this project serves as an interdisciplinary link between biology and physics, I presented my work at GK-12 Building Bridges: Integrating Math, Science and Engineering on the South Plains. I was also invited to participate in a panel on trans-disciplinary research at this conference.
For my work on this project I received the 2013 Honors College Collaborative Learning Award.

Friday, September 7, 2018

Jesus was stabbed in the stomach

Blood mixed with water flowed out of Jesus' spear wound because he was stabbed in the stomach (probably).

We have almost no detailed information on the location of Jesus' spear wound. However, we do know three things:
1. The spear head must enter the "side", which could mean anywhere on the lateral aspect of Jesus' abdomen or torso.
2. Jesus was elevated on a cross, therefore the spear thrust would have been at an upward angle.
3. Blood mixed with water exited the wound.

There are numerous complicated scenarios in which water could have exited through the wound along with blood--most notably a pleural effusion that built up from a previous injury. These scenarios are less likely because they require an additional hypothesis (that one of the previous injuries caused abnormal fluid buildup in one of Jesus' body cavities, and this was later pierced by the spear).

But there are two situations that do not require an additional hypothesis. There are two locations where "water" builds up under normal circumstances--the stomach (Figure 1) and the bladder.

A spear wound to the bladder is so unlikely that it is hardly worth mentioning*.

A spear wound to the stomach is extremely likely (Figure 1). First, a spear wound that entered Jesus' stomach definitely would have been described as a spear wound "to the side". Second, the elevation of Jesus and the upward angle of the thrust favors a stomach wound (Figure 2). Third, Jesus had fluid in his stomach (beyond the normal gastric acid that is always present):

"28After this, Jesus, knowing that all things had already been accomplished, to fulfill the Scripture, *said, “I am thirsty.” 29 A jar full of sour wine was standing there; so they put a sponge full of the sour wine upon a branch of hyssop and brought it up to His mouth. 30 Therefore when Jesus had received the sour wine, He said, “It is finished!” And He bowed His head and gave up His spirit." (John 19:28-30)

Figure 1. Spear thrust to the stomach. Modified from http://healtharchives.info.

The stomach wound scenario is so obvious that I cannot fathom how it isn't widely accepted as the leading hypothesis for Jesus' spear wound.


If Jesus had died from previous injuries, there would have been fluid in his stomach, and the spear would have caused that fluid to mix (at least partially) with blood. If Jesus were alive, the same thing would have happened.

In fact, the stomach would have been hard to miss using an upward thrust to the side of an elevated victim. Check out a horizontal cross-section of the upper abdomen (Figure 2). Because the spear was traveling at an upward angle into an elevated victim, the horizontal plane is especially helpful for illustrating what organs would have been in the way of the spear thrust. The primary target (that definitely would have produced blood mixed with water) is the stomach.

Figure 2. Stomach outlined in green. Modified from http://www.netanatomy.com.

Conversely, at an upward angle, a spear thrust would have difficulty passing directly between two ribs (the more vertical the angle, the harder it would be). This isn't to say that a spear thrust couldn't break ribs (it could), it's just less likely than a stomach wound (which wouldn't have needed to either "thread the needle" or break ribs). This is especially true if the spear had a broad head. And again, the scenarios in which "water" is mixed with blood require additional hypotheses for thorax wounds. A stomach wound scenario does not.

A spear wound to the heart would have released SO MUCH blood  that it is unlikely that observers would have been able to appreciate any "water" coming from the wound, even if fluid had built up somewhere (unless it was a very large amount of fluid--which again requires far more mental gymnastics than a simple stomach wound). Observers definitely would have noted the watery appearance of fluid emanating from a stomach wound.

In conclusion, by far the most likely scenario is that Jesus was stabbed in the stomach.


The bladder-wound scenario
*Because Jesus was elevated on the cross, a spear wound thrust upward would have needed to enter Jesus' leg and travel upward to eventually pierce his bladder, and it would have needed to pass through thick bones to do so. This did not happen.

But the stomach is only on one side!
 True. Only wounds to Jesus' left side fit with this scenario. Similar wounds to the right side of Jesus' body would have hit the liver, which would not have resulted in "water" mixed with blood exiting the wound.

What about hitting both the stomach and the heart?
A spear thrust could go all the way through the stomach and then enter the heart. This definitely would have killed Jesus. However, this scenario is less likely than a simple stomach wound.