Category: BioTechnology

Defining & Finding the Higgs Boson Particle

BioTechnology, Blame the Media

I know that I love on the BBC quite a bit, I make no bones about it being my preferred source for daily science news coverage. However, the article “LHC has two years to find Higgs” is an unfortunate departure from the BBC‘s typically stellar science coverage.

The article caught my attention because I’m already familiar with the Large Hadron Collider (LHC) a particle collider operating underground along the France/Switzerland border. A particle collider takes protons (a small part of an atom), runs them around at speeds close to the speed of light, and crashes the particles into each other. Hence the name, particle (the protons) collider (the smashing them together part.)

The other part of the BBC article’s title that caught my eye was “Higgs” which refers to the Higgs Boson Particle. The Higgs is a theoretical particle – meaning that it is a particle that physicists THINK exists, but they don’t actually know for sure, it might not exist at all. In trying to understand the universe and what gives all matter mass, physicists have come up with several theories.

One of these theories is the Standard Model – which is based on the existence of the Higgs. If it exists the Higgs would explain how particles get mass. The LHC is looking for the Higgs by analyzing the teraelectronvolts (TeV – a measurement of energy) that would be emitted by the process through which particles get mass. The LHC should be able to detect the TeV of the Higgs – if it exists.

Part of one LHC tunnel. Source: Wikimedia Commons

I realize that the BBC’s article is clearly an update piece about ongoing research, but it just glosses over some very important explanations about the LHC and the Higgs. If I didn’t know that LHC was a particle collider or that the Higgs is a theoretical particle I would have no idea what this article is about from the title. Even as you go through the body of the article, there is no background information. To say that particle physics is complicated is an understatement. All the more reason why this article needs background information to make it understandable. As it is, this article is not appropriate for lay audiences.

The timely component of this article, or the reason why an update on the LHC is needed, is that researchers have announced that if the Higgs isn’t detected by the end of 2012 they will conclude that the particle does not exist. If the Higgs doesn’t exist then the Standard Model is not the way by which the universe is organized, meaning researchers would have to re-define their understanding of sub-atomic physics.

This is a news worthy update, however I feel like the reporter didn’t do the story justice. Even the quotes do nothing to explain what LHC is, what the Higgs is, or what the significance of its existence or non-existence would be. I have a particular problem with the paragraph:
“According to Professor Tom LeCompte of the Argonne National Laboratory, US, who works at the LHC: “The most likely place for the Higgs to be is in a very good place for us to discover it in the next two years.”

I have no idea what this quote means. “The most likely place for the Higgs to be is in a very good place…” What? My best guess is that the scientist is trying to say that research at LHC has progressed to the point that if the Higgs isn’t detected in two more years, it doesn’t exist. But obviously, that is NOT what he actually said.

This is a prime example of a quote that shouldn’t have been used. Rather than just using the confusing quote the reporter could have asked the source to clarify or say what they meant in a different way. The reporter could also have paraphrased what the researcher was trying to say. Just because an intelligent and successful scientist makes a statement, doesn’t mean that statement is gold. As a writer you have to decide what quotes add to the story, and what quotes are just confusing. You shouldn’t put in quotes just to have quotes.

I realize that this is just a short article and it isn’t trying to do an in depth analysis of the LHC, the Higgs, or particle physics, but that doesn’t mean that background information and good quotes should go out the window. This topic is particularly complex and nuanced, and I’ve struggled to provide a decent explanation here – but just because something is hard doesn’t mean you don’t have to even TRY to explain it clearly.

I think the BBC article could have been a lot better if more effort was put into trying to at least define the LHC and the Higgs for the reader. After all, the reader isn’t going to care that some particle might not exist if you don’t explain what that particle is and why it matters.

If you want to learn more about the LHC, I can’t help but recommend the following video. I still get a kick out of watching physicists try to rap and dance. You will find the explanation of the Higgs in the video far more complex than mine. Physics is out of my realm of comfortable understanding – but I gave it a shot and tried to keep it as basic as possible.

Humans Contaminate DNA Databases

BioTechnology, Genetics, Government Regulations, New Research, Past Articles, Research Funding, Science Policy, Sequencing

Interesting research has been published in the online journal PLoS One, describing a problem with contamination in non-human DNA databases. DNA databases are libraries of genetic information about specific species. When a species has its genome sequenced, its genetic data goes into a database so that other research can be conducted based on that known genetic information.

When a DNA database becomes contaminated it means that there is other information that has corrupted the data stored in the database. In the new PLoS One paper the researchers (from the University of Connecticut) evaluated human contamination of databases that were supposed to contain other species – like the zebrafish. So contamination occurs when human DNA gets incorporated into the database for another species. When researchers go to work with the data about the zebrafish for example, they are actually working with human data without knowing it.

The University of Connecticut researchers looked for human contamination in NCBI genome databases, the University of California Santa Cruz (UCSC) databases, and the Joint Genome Institute databases. They found human DNA where it shouldn’t have been in a total of 492 of 2,749 evaluated databases.

This contamination issue is extremely problematic because research conducted based on contaminated information can not be trusted to be accurate. It can also be very difficult to track down which databases are contaminated unless the resources (time, money, etc) are spent to evaluate databases for clarity – as was done in this new research.

Database contamination is a relatively new issue brought to light be the massive influx of new genetic information made possible by improved genome sequencing technology. A similar issue that has existed for decades is cell line contamination which occurs when cells that are suspended in culture (alive outside of the body) are contaminated with cells that aren’t supposed to be there.

No regulatory body has stepped up and put a stop to cell line contamination in the last thirty years. I just hope that database contamination doesn’t follow suit.

To learn more, read the paper about Database contamination, or read an article I wrote for BioTechniques about cell line contamination. As taxpayers we spend a lot of money to fund scientific research, so it is important to know what problems (like contamination) exist in the research community.

Sequencing Genomes to Save Species

BioTechnology, Conservation, Environment, Genetics, New Research, Sequencing, Zoology

For this post I’m trying something a little different. I mentioned a few weeks ago that I’m using Science Decoded for class, and as a part of that we were assigned to write a post in the form of a list.

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All living organisms are made of DNA, a series of nucleotide bases (Adenine, Guanine, Cytosine, and Thymine) contained in chromosomes. Genome sequencing is an analysis of DNA, conducted by “reading” the different patterns of nucleotides A-G-C-T for differences between species, and abnormalities within a species. Researchers around the world are working to sequence the genomes of a variety of organisms, including those on the endangered species list.

1. Orangutan (Pongo abelii) – In January 2011 the National Institutes of Health (NIH) announced the publication of the orangutan genome sequence. Funded by the NIH, researchers from Washington University School of Medicine in St. Louis, MO and Baylor College of Medicine in Houston, TX sequenced the genome of a female Sumatran orangutan, five additional Sumatran orangutans, and five Bornean orangutans (Pongo pygmaeus.) The research shows that orangutans share 97% of their DNA with humans, but compared to humans and chimpanzees, orangutans have evolved much slower leading to fewer mutations (variations in the code between individuals of a species). (Read more) 

2. Tasmanian Devil (Sarcophilus harrisii) – Fifteen years ago a facial cancer was identified in tasmanian devil populations. The cancer has ravaged the species, resulting in an 80% decline that has forced the species to the brink of extinction. This cancer is transmissible, which means that biting the face of an infected animal passes it between individuals. In September 2010 researcher from the Wellcome Trust Sanger Institute and the genome sequencing company Illumina announced that they sequenced the tasmanian devil genome in an attempt to learn more about the cancer and how to stop it from wiping out the species. (Read more)
3. Giant Panda (Ailuropoda melanoleuca) – Arguably one of the cutest endangered species, the giant panda is a prominent symbol of China, where it lives in a restricted mountain area. According to the Beijing Genomics Institute (BGI) the number of giant pandas left in the wild is estimated between 1600-3000. In December 2009, BGI published the complete sequence of the giant panda genome. With the information obtained by the genetic analysis researchers hope to learn more about the genetic and biological factors that shape this species behavior to assist in disease control and conservation efforts. (Read more)

4. Tibetan Antelope (Pantholops hodgsoni) – Listed by the United Nations as an endangered species since 1979, the Tibetan antelope could hold the key to understanding the pathogenesis of chronic plateau sickness. The species calls China’s Qinghai-Tibet Plateau home, making them ideal for studying the evolution of species that thrive in environments characterized by extreme cold and low oxygen levels. The genome sequence of the Tibetan antelope was announced in December 2009 by researchers from BGI and Qinghai University. (Read more)
5. Coral Reefs (Acropora millepora) – Coral reefs are among the world’s most diverse ecosystems, yet according to the Genome Center at Washington University it has been predicted that in the next 50 years between 40%-60% of the world’s coral reefs will die. In 2005 the NIH funded the sequencing of the coral A. millepora (which is not an endangered species, though coral reefs as a whole are endangered ecosystems) to serve as a “lab rat” for studies of the environmental factors (light, sediment load, or acidity) that can cause coral death. (Read more)
Not quite endangered & not fully sequenced:
6. Polar Bear (Ursus maritimus) – Recently removed from the list of endangered species recognized by the United States, researchers at BGI are still working to sequence the polar bear genome. The polar bear sequence is a part of a three-pronged project to sequence the Tibetan antelope (completed in 2009) and emperor penguin genomes.

7. Emperor Penguin (Aptenodytes fosteri) – One of the most recognizable penguin species, the Emperor Penguin is found in Antarctica. The emperor penguin is currently under consideration for inclusion under the Endangered Species Act, due to the effects of climate change. The genome sequencing project is being conducted by researchers from BGI in conjunction with sequencing the polar bear, and Tibetan antelope genomes. (Read more)
8. Snow Leopard (Uncia uncia) – In October 2009 researchers from Oregon State University, the Western University of Health Sciences, and the Miller Park Zoo (IL) announced plans to sequence the genome of the snow leopard (which is on the Endangered Species list). According to Oregon State, the snow leopard is prone to diseases that do not plague other big cats including pneumonia, enteritis, hip dysplasia, and papillomaviruses. Sequencing the genome could help researchers identify what makes the snow leopard susceptible to these disorders. (Read more)
Genome sequencing technology continues to develop, making it easier and cheaper to sequence the genomes of various organisms. While an endangered species has yet to be saved due to the information obtained by sequencing its genome, what researchers learn will help them gain a better understanding of endangered species, which is a step in the right direction towards improving conservation efforts. 

Technology Takes A Look At A Pliosaur Skull

BioTechnology, New Research
Source: Flickr

The article “Colossal pliosaur fossil secrets revealed by CT scanner,” caught my attention because it describes an interesting new use for existing technology. Researchers took the skull of a pliosaur, a creature that lived in the oceans during the Jurassic period, and scanned it to learn more about the fossil remains – which may belong to the largest pliosaur yet to be discovered.

The creature is estimated between 10-16m, based on the skull which is 2.4m long. By comparison, a killer whale is 5-8m and a human is only 1.5m. Needless to say, these things were big. According to the BBC article, a pliosaur would have had the jaw strength to bite a car in half.

The CT scanner used for the research belongs to the University of Southampton in the UK. The machine is one of the largest of its kind, which was necessary to beam through the dense fossil to form a 3D image of what the inside of it looks like. The findings may be able to help researchers establish if their fossil is a different species, or just an abnormally big example of a pliosaur. 

Help Me Obi Wan Kenobi

BioTechnology, New Research

My experience with holograms doesn’t extend much farther than Princess Leia’s secret message to Obi Wan Kenobi, entrusted to R2D2 in the first Star Wars movie released (but really the fourth story in the series) A New Hope. Yeah, Nerd Alert, I’m OK with it. Anyway, Star Wars has shown us that holograms are something used in a galaxy far far away, certainly not here on Earth, and certainly not in present day. But alas, Star Wars has led me wrong.

Source: Wikimedia Commons.

New research from the University of Arizona is close to making holograms a reality. So far, the group is able to film a video image and beam it to a new location where it updates in “near” real-time. The research team has been working to improve the speed at which the images are conveyed, and has gotten them as fast as every two seconds. Video with a continuous flow of images, like Princess Leia’s famous message, is just around the corner.

The BBC article by Jonathan Amos, “Hologram messaging coming of age,” breaks down the process like this:
1. A series of cameras arranged in a semi-circle take multiple images of a person or object from lots of different angles.
2. The images are fed into a computer, where they are processed and then sent to another computer at a different location
3. A specially designed 3D printing system receives the images and based on the information contained in them, controls a laser that “writes” the images onto a screen made of a special plastic.
4. The special plastic screen can update every two seconds, but a light source is needed to be able to see the changing holograms.

The researchers say that holograms will be useful for manufacturing, to update plans or blueprints as workers are designing new models. I think it has value simply for being cool and for proving to Star Wars geeks that IT COULD ACTUALLY HAPPEN, well at least the hologram part.