Thinking of moving operations to Blogger via JustScience.co.vu

I’ve been thinking about this for a long while. I have had a Blogger site up for a while and I think it is time to make the complete transfer. I love the community of WordPress, but I don’t like the restrictions for free users like myself. So, visit JustScience.co.vu and take a look. Please let me know what you think.

Thanks.

Dolly Parton’s Best Assets: Compassion and the Imagination Library

Dear Imagination Library Graduate,

My, how time flies. It seems it was only yesterday when your family and friends read you your first story. You were just a baby. Now you’re five years old and about to go to school. How exciting!

This may be your last book from my Imagination Library but you have to promise me you will keep on reading. If you go to your local public library you will find a great number of books just for kids your age. Every book is a treasure and every time you open one up you will meet new friends and take wonderful journeys to magical places.

I hope you have a great time in school. I bet your school will even have a library where you can check out books. You and all of your friends are very special. There is no limit to what you can do or how far you can go. Just remember the lessons my family taught me – dream big dreams; learn everything you can learn; and care for all those who care for you. You do all of these things and you can be anyone you want to be.

You are terrific, and remember…

I Will Always Love You,

Dolly

This is the letter from Country Music Legend Dolly Parton on the first page of the 60th and last book given to each child from her Imagination Library. Most of us know Dolly Parton from her decades of music, books, and films, but Dolly comes from very humble beginnings in the foothills of the Great Smoky Mountains in East Tennessee. Her life story is a true Cinderella story and is nothing short of amazing; one of twelve children born to a tobacco farmer living in a one room cabin. A replica of this cabin resides at Dolly Parton’s themepark, Dollywood, the largest employer in the county and host to over 2.5 million visitors each year.

Dolly never forgot her home and her family. I live in Knoxville, TN; about an hour from Dollywood thanks to traffic. Having worked at a local hospital, I know Dolly is known to regulary visit hospitalized family members (which there are many). Perhaps much less known, Dolly gives back to her community in many ways mostly through the Dollywood Foundation. This includes the largest bald eagle sanctuary in the country located at Dollywood.

Dolly’s Imagination Library started small with a simple goal: give each child in her home county a free book each month from birth to age 5. The idea quickly took off. In 2000, the program was opened up to any community willing to support it. In 2004, Tennessee Governor Phil Bredesen started Books from Birth, expanding the Imagination Library statewide. Within a couple of years, research began to accumulate showing the impacts Imagination Library has on families and the learning skills of the children (check here).

My daughter has looked forward to each new book each month and I know many children feel the same way. Through Dolly Parton’s Imagination Library, children’s dreams, imagination, and creativity are nurtured and celebrated while increasing each child’s love of reading and learning. These combined give me hope these children can do much more with their lives than us.

Thanks, Dolly.

Imagination Library
Imagination Library (Photo credit: United Way of Greater St. Louis)
2013 Imagination Library Launch
2013 Imagination Library Launch (Photo credit: United Way of Greater St. Louis)

News Flash: Cook Your Chicken (like you have been)

I personally have a Google News section for “Bacteria”. I was shocked by the headlines I have read today:

After being told for years not to eat raw chicken, yet again, we are reminded why.
After being told for years not to eat raw chicken, yet again, we are reminded why.

How is this news? We have a general understanding around our house, “Raw chicken is the dirtiest thing you can bring into the house”. Even my four year old knows this. Through many years of research, countless studies have shown the quick adaptability of bacterial species to the over use of antibiotics. This has rendered most common drug treatments for bacterial infection useless.

However, bacteria have NOT adapted ability to resist some common treatments like alcohol, bleach, UV radiation, and heat. I do not recommend cleaning tomorrow night’s chicken with alcohol or bleach. I personally would go with heat. So, please, next time you want to make a chicken dinner, be safe and cook it as recommended.

E. coli Up Close and Personal: Scientific Rockstar and Public Enigma

This is an article created as guest post for Kitchen Table Science.

It seems nothing puts fear in the hearts of the masses like mentioning E. coli. Most think of the disease-causing germ that contaminates everything from spinach to beef. I agree the strain Escherichia coli O157:H7 and its cousins O26, O145, STEC O104:H4, and others, are a wretched bunch that give the whole species a bad reputation. What makes these strains so vile are the extra proteins encoded within their genome. For example, E. coli O157:H7 has a larger genome coding for 5561 proteins while the parent strain E. coli W codes for 4739 proteins. Thus is the life of a bacterium. The fact there are so many bacteria means they are usually in close proximity to each other. Physical contact between bacteria, not just those of the same species, allows for the transfer of genetic material between two cells (horizontal gene transfer); the closest thing to sexual reproduction you will find for prokaryotes. If the genes transferred to the recipient give it an advantage or new ability that helps it compete and thrive in its environment, they will remain in the genome. Otherwise, they will be discarded after genome compaction.

Most E. coli are completely harmless and, in fact, beneficial. If the general public knew more than what was broadcasted on the 24 hour news channels, they would see the tiny rockstar scientists have known about for some time now. Beginning in earnest in the 1950s, E. coli is easily cultured in laboratories and very cheaply. Its quick generation time (20 min. at optimum temperature) made it a great model organism to study in many fields of science and medicine. This organism is the work horse of biotechnology due to the relative ease of manipulating its genome or adding complete genetic circuits into the cell using plasmids.

Sidebar

Even after 50 years of intense research, E. coli still holds many unknowns out of the reach of our knowledge. Like all other sequenced genomes, there are a number of “hypothetical proteins” and “proteins of unknown function”. This means by our best abilities, we can locate parts of the genome that code for proteins, however, this doesn’t mean we are able to understand the function of a particular protein.

Image courtesy of Predrag Radivojac. Thanks, Pedra.

The above shows just how much work is left to understand the biological capabilities of Mother Nature. Short version: over 40 gene sequences in databases, but the number of which that we know what the function is holding steady around 500,000 and the number of solved protein structures is over 100,000. This is a growing gap between the known and unknown.

 Where would we be without E. coli?

One advantage of E. coli is their effect on our immune system. Some may find this counter-intuitive, but E. coli can lower the workload of our immune system when pathogens are present, especially in the intestine. When E. coli attach to the GI wall, it changes the acidity of the lining thus making infection from other bacteria less likely. Another benefit is in overall digestion. E. coli promotes better breakdown of food thus preventing accumulation of waste which is a major cause of bloating and constipation.

Many outside the scientific community may not be aware of how integral E. coli are to the advancement of many fields including medicine, pharmacology, biology, and even human physiology. Another reason to not believe the hype.

“Groundbreaking” ‘Duon’ Paper Only Continues Research From Prior Studies

There is a lot of chatter on the internets about the press release from the University of Washington about a paper published in the journal Science this week. One claim within the press release is that findings in the present study uncover a ‘hidden’ code within human DNA that scientists had no prior knowledge of. As many have written, this assumption is completely false and grossly exagerated.

After reading the paper (paywall), I can say the study does add a wealth of new information to an already known phenomenon. I recommend reading the article if one is in the molecular biology or human genetics fields. However, the press release about this study should be retracted for the amount of misleading claims raised within it.

In fact, the authors write in the final paragraph,

Our results indicate that simultaneous encoding of amino acid and regulatory information within exons is a major functional feature of complex genomes. The information architecture of the received genetic code is optimized for superimposition of additional information (3435), and this intrinsic flexibility has been extensively exploited by natural selection. Although TF binding within exons may serve multiple functional roles, our analyses above is agnostic to these roles, which may be complex (36).

Pay close attention to the parenthetical numbers within the quote. These indicate the statement is referencing a prior publication. 34 is reference to a paper from 2007 in Genome Research entitled, “The genetic code is nearly optimal for allowing additional information within protein-coding sequences.” and can be found here. 35 is a paper from 2010 also in Genome Research; “Overlapping codes within protein-coding sequences.” found here. And 36 is from Nature Genetics earlier this year entitled, “DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements” found here.

A question for UW Today,

If these authors uncovered an unknown, hidden code within DNA, how could they reference earlier studies that essentially elaborated upon these same ‘secrets’?

I’ll be waiting for an answer…

Repeat after me: There is no newly discovered hidden code in DNA.

It is a very sad and unfortunate occurrence when newly released research findings are hyped and overstated. This week the University of Washington Office of News & Information released a press release embarrassingly called “Scientists discover double meaning in genetic code“. Since then, the release has been picked up by websites across the globe. In that way, the press release did its job. Unfortunately, the statements within the release along with the title have done a world of harm. I can only hope it was unintended.

The release starts by stating scientists discovered a second code hiding within DNA.

This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

This ‘second code’ will not change anything scientists do regarding studying DNA. This ‘hidden second code’ has been known and studied for decades.

Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins. UW scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long.

Let me rewrite this paragraph to make it factual:

Since the genetic code was deciphered in the 1950s, scientists have continued to find additional layers of complexity in the regulation of how genes are transcribed to make proteins. The current study from UW scientists have added additional knowledge to this growing field.

This is the most unfortunate part:

“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Stamatoyannopoulos. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”

This release was written by writers in a news department as a marketing piece, but when the scientist also grossly exaggerates the findings, it is very sad. Like Emily Willingham said in Forbes, “I can only hope that Stamatoyanopoulos didn’t really say that”. Scientists have not made any such assumption and have decades of evidence to the contrary.

The study shows that changes in the DNA sequence can have two-fold consequences upon the protein made from it. It can change the amino acid sequence of the protein and change which proteins bind that help transcribe the DNA into the RNA used to create the protein. This is not new. The finding that made this study worth of the prestige of publishing into Science is the frequency of the DNA code that is used to determine which proteins bind to the DNA to create the right form of the protein. These proteins, known as transcription factors, have been known for decades and bind to a number of DNA sequences to ensure the cell creates the exact protein needed.

As is common in press releases, the last part of the piece tries to explain DNA and the language of genes. In this aspect, the release does an even worse job:

The genetic code uses a 64-letter alphabet called codons.

The genetic code uses 64 different combinations of nucleotide sets of three, called codons; most of which code for one of the twenty amino acids needed to make a protein.

I could keep going, but I’m exhausted by trying to set the record straight.

Are we completely wrong about autism? Are we the abnormal ones?

I was home today with the TV on. It was Ingenious Minds day on the Science Channel. A majority of the people showcased on the shows hadAutistic Spectrum Disorder, or ASD. After watching/listening to several episodes, something occurred to me as I was making dinner, who is to say we are the ones with an abnormal brain? Historically speaking, it would be very unlikely for the majority of the population to be abnormal.

But what if this was looked at from a different perspective? The growing prevalence of diagnosed autistic children could be observed as a rapid evolution of the human. Let’s say Mother Nature’s evolution experiment with humans. I have written about autism elsewhere (here) and how much of this disorder is a huge question mark to researchers. Progress is being made with university PR departments and other ‘media’ proclaiming it is all just a intestinal flora imbalance and is curable. Evidence supports a link between gut bacteria and several disorders, but it is immature to call it case closed.

I am left looking at this as naivete on our part. The autistic are the abnormal ones because we don’t understand their physiology. I just hope our descendents don’t look back at us ashamed of our folly.