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Genomes, Intraterrestrials and Tissue

October 7th, 2010 by Jessika

DNA Sculpture (Photo by mira66 via Flickr)

For thousands of years, humans have been curious. That curiosity has led us to advances in technology and scientific discoveries. Fortunately, humans today are just as curious.

This week I read about people near and far who continue to put their urge to ask questions to good use.

So, let me start with a relatively recent discovery that led to many more questions than answers.


Ten years ago, scientists fully sequenced the first human genome. Today, more than 20 human genomes have been sequenced. But despite this huge scientific leap, many questions remain unanswered. In Erika Check Hayden’s “Life Is Complicated,” she explores just how much we do and don’t know about ourselves.

She asks “can one ever truly know an organism – or even a cell, an organelle or a molecular pathway – down to the finest level of detail?” No.

Like all experiments, testing one scientific hypothesis opens the floodgate to countless other hypotheses. The Human Genome Project was no exception.

“The more we know,” said Jennifer Doudna, a biochemist at the University of California, Berkeley, in the piece, “the more we realize there is to know.”

Hayden cites the story of the oft-studied protein p53 as an example. The protein was originally misidentified as a promoter of cancer. But after more study, it was discovered that the protein actually does the opposite, marking cancer cells for death. Scientists are still unveiling the protein’s secrets. Its interaction with chemicals and DNA and RNA has proved highly complex.

When you step back and take a look at the human body, it’s simply amazing. Perhaps a better way to say that would be complexly amazing. To think that we have these proteins working right now looking for damaged cells and  that in those cells our DNA and RNA are transcribing, really does make me pause. There is so much that needs to go right for me to be healthy. But at the same time there is so much that can go wrong.

The article also mentioned the tale of systems biology, a discipline developed to make sense of complicated interactions. Biologists in this field have run in to problems since its start. The systems are too intricate for scientists to get all the data they need for analysis! This definitely would be discouraging to researchers in the field. At the same time, though, it’s a good thing that life is hard to fully understand. If it were easy, scientists would have nothing to do, and there wouldn’t be anything to fulfill our thirst for knowledge.

“Life Is Complicated” came in a package of stories for Nature about the human genome. The second story I must admit was a little less interesting. “The Human Race” briefly looked at the players in the race to sequence the first human genome. There seemed to be so much drama in this race, but this short piece didn’t wring out that drama fully. Instead, it just presented short segments on each of the racers almost like the brief bios you get in a program before a play.

The third part of the package, “The Sequence Explosion,” helped to visualize gene sequences and the human genome, providing an interesting graph of the number of human genomes sequenced along with the increasing technology and the reduction in cost to sequence those genomes. While this graph, along with essentially pie charts of the amount of non-human vs. human DNA sequenced, were interesting, I definitely found the anchor article much more engaging.


One of my latest pieces has taken me to the wonderful world of deepwater microbes. So, I was very excited to read “Blurring the Lines Between Earth and Life” by Terah DeJong. The piece took me even farther down than I had gone before to the life in the Earth’s crust. I met the intraterrestrials.

What’s so fascinating about these microbes is that so little is known about them. Few scientists study them and even fewer would spend years on a boat with other scientists, working 20 hours a day to analyze sediment from the Earth’s crust. But Katrina Edwards, a geomicrobiologist at the University of Southern California, loves intraterrestrials so much that she would do just that. In 2009, she along with 21 others began a 10 year expedition between the Caribbean and West Africa to uncover some of the mysteries these fascinating microbes.

DeJong’s article introduces us to Edwards, her colleagues and the intraterretrials in this easy-to-read piece. The writing really made me want to keep reading. Her descriptions throughout revealed so much about a story that would have been easy to get bogged down in.

For example, DeJong describes Edwards as someone who “still goes wide-eyed at the thought, once controversial but now widely accepted, that most life on Earth is intraterrestrial.” That description tells the reader so much. It even made me picture Edwards talking to students or friends about intraterrestrials with her face lit up like a child on Christmas morning. I wish I knew what fascinated me like that.

The only frustrating thing about this piece is that I want to know what Edwards and her colleagues find on their expedition. I don’t know if I can wait 10 years.


The Steve Silberman article “Tumors. Blood. Organs. How the raw materials for 21st century medical breakthroughs are spoiled by outdated technology.” explores the frighteningly behind-the-times world of American biobanks, companies that preserve human tissue for medical experimentation.

Biobanks get to regulate themselves, and the inconsistency between each bank’s practices has dire consequences. I found this surprising. Why do biobanks not have to adhere to set government standards? There’s no uniform way of cataloguing tissue and samples continue to be preserved in old standbys like glycerol and dimethyl sulfoxide, DMSO. Why haven’t new preservatives been developed? Allison Hubel, a cryopreservation expert at the University of Minnesota, said in the article that “there is no motivation for funding.”

But the industry should be motivated, because the preservatives currently in use have been found to damage samples, making the data gleaned from them unreliable and inconsistent.

This lack of government regulation leads to problems with the samples, making many of them unsuitable for use. The article cited a bank at a university that supposedly had 12,000 samples of glioblastoma, an aggressive brain cancer. Only 18 of the reported 12,000 could be used. After appealing to banks around the world, researchers studying glioblastoma could not even get 500 samples. That’s appaling.

Perhaps just as scary is the thought that many of the tissue-based studies may have inaccurate results because of poor sample quality. That really makes me wonder how much of the research out there we can really rely on. Does this mean we have developed treatments based on faulty findings? Possibly.

Tissue based research is essential, and without proper regulation and updated techniques, biobanks put that research in jeopardy. Where’s the government when you need it?

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