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How similiar are chimps and humans? April 30, 2010

Posted by Kyle in Behavior, Biology, Ecology, Evolution.
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Many researchers are interested in what makes chimps and humans different, as well as the similarities. A recent article on Science Daily highlighted two studies published in Current Biology on how chimpanzees deal with death.  The first study shows that chimps may have a more developed awareness of death than once thought.  Researchers observed how chimps responded to dying and dead chimps of their group.  In some cases, mothers would continue to carry and care for young that had died.  Researchers also observed how a group of chimpanzees responded to a dying female in the days leading up to her death.  They found that there were similarities between the chimps behavior towards the female and human behavior when an elderly relative is dying.

Chimp mother carrying mummified infant

Since chimps are our closest evolutionary relative, it makes sense that they would share some things in common with us.  In the second study researchers found that mothers would continue to care for their dead young, even months after the infant had died. As time went on, the mothers slowly began to separate from the corpses. These observations seem to indicate that there is a close bond between mother chimps and their young.  As Dora Biro of the University of Oxford points out, chimps resemble humans in many of their cognitive functions.  How chimps react to death and are affected by it could shed light on the evolutionary origins of human comprehension of death.

The similarities between humans and chimps starts with DNA.  Humans and chimps have very similar genomes. In fact, over 98% of a chimps DNA is the same as a humans, with most of the differences being in non coding regions. Another article on Science Daily addresses this similarity. According to Katherine Pollard, assistant professor at the UC Davis Genome Center and the Department of Statistics, the differences between humans and chimps is in how we use our proteins, not in the actual proteins.  Pollard and other researchers found “highly accelerated regions” of DNA when comparing the DNA of humans and chimps. These highly accelerated regions were areas of DNA that had evolved, however only a few of these regions contained genes coding for proteins. Researchers believe that one region may contain a gene important for brain development. As different as chimps and humans appear, there are more similarities than most people realize.

There are many researchers that have highlighted key similarities and differences in humans and chimps. With more research comes more interesting discoveries linking us to our evolutionary relatives. Some other interesting similarities have been pointed out recently, such as the understanding of fire as well as culture among different groups of chimps. More interesting articles on current research can be found on Science Daily.

Gattaca… is it now a reality? April 30, 2010

Posted by Jill in Biology, Genetics, Health, Medicine, Policy.
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Lego DNA helix

For anyone who has seen the movie Gattaca, the concept is mind-boggling. Could molecular genetics really go as far as artificially selecting for so traits as specific as having an innate ability to speak or play the piano or be a world-class swimmer, not just choosing for a tall blond-blue eyed baby? In the movie Gattaca, Vincent is one of the last “natural” babies born into this genetically-enhanced world, where life expectancy and disease likelihood are determined at birth. Myopic and scheduled to die at 30, he has no chance of pursuing a career in a society that now discriminates against your genes, rather gender, race or religion. He assumes the identity of Jerome, a world-class swimmer who was crippled in an accident, in order to achieve prominence in the Gattaca Corporation, a spaceflight company, where he is chosen for his lifelong dream of being on a manned mission to Saturn.

Although this movie is fiction and was produced in 1997, how far away from this society are we really? The Stanford University School of Medicine analyzed a healthy person’s DNA in an attempt to predict the long-term diseases or medical conditions he would face in the years to come. The genome was of Stephen Quake, who is the Lee Otterson Professor of Bioengineering. The thought is that along with a family medical history, patients could potentially have a genetic component to their medical history that would help physicians in determining whether or not certain medications will work or have adverse side effects for that patient based on their genetic makeup. Patients that are at a potentially higher risk for a certain condition or disease will be able to have closer monitoring of that condition through testing or observation even if not present in the patient. Another benefit to this form of “pre-screening” of genetic disorders is that it will be more cost effective and be more economically sound because it will reduce the prevalence of unnecessary tests, making medicine more efficient.

In conjunction with bioinformaticians, Atul Butte, MD, PhD, assistant professor in bioinformatics, and his lab members have already done a lot of the necessary leg work for interpreting the genetic code into something meaningful, like what individual codons or even base pairs mean in a particular part of the genome. They spent 18 months cataloguing publications that associated particular genetic changes called SNPs (single nucleotide polymorphisms) with effects on specific diseases. It was the first time anyone had compiled all the information in one database.

Upon receiving the genome of Steve Quake, researchers were able to create an algorithm that analyzed all of the data they had compiled from previous studies against Quake’s genome to determine his risk factors for certain conditions such as obesity, Alzheimer’s, type-2 diabetes, and prostate cancer. They determined Quake’s risk of prostate cancer is about 23 percent, risk for Alzheimer’s diesease is 1.4 percent due to protection, and type-2 diabetes, coronnary artery disease, and obesity all at 50 percent. This information raises questions of patients actually knowing these alarming statistics because they are afraid of living their everyday lives. I’m sure this is similar to the idea of life insurance companies providing you the statistics for the likelihood that you will die if you walk across the street to your daily job. Most people do not want to know these things and if the problem arises, they will deal with it then instead of relying on knowing odds to predict what could potentially happen to them.

This new scientific research raises many ethical questions like should this be implemented to aid patients or should it be optional or is this an exploitation of personal information? As more of these findings are published, there will certainly be more controversial discussion in terms of what is right and wrong in exploring the meaning of our genomic fate.

The whole article can be found here.

Cities Going Green April 30, 2010

Posted by Kyle in Environment/Conservation.
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Recently the Marian University Science Club celebrated Earth Day by showing Avatar and providing free recycling bins on campus.  Now that Earth Day has passed hopefully at least a few more students around campus have an increased awareness of their impact on the environment.  It seems that every year more and more people are getting involved in Earth Day activities, and it has definitely caught my interest. While doing a little reading on the internet I came across the Earth Day Network.  The Earth Day Network is an organization that was founded to strengthen the environmental movement not only in the United States, but all over the world.  According to their website, they work in 190 countries and over 1 billion people around the world participate in Earth Day activities.  After reading a little about what they are doing around the world to address environmental issues, I started to look at what some people are doing here in Indiana.

The first thing I noticed was a news article on recycling in the city of Indianapolis.  Recently city leaders have been working to provide curbside recycling to all residents, possibly free of charge. This would be a huge change for Indianapolis, since residents who currently want curbside recycling have to pay a fee for the service.  The article also points out that currently in Marion County, less than 10% of waste is recycled.  Hopefully this number can continue to climb in years to come with the help of city and community leaders. I’m sure many citizens of Indianapolis, including myself, would welcome a free curbside recycling program.

Indianapolis is not the only city in Indiana working to go green.  In a related article, Muncie officials also have plans in the works to clean up at least one part of the city. Recently The South Muncie Redevelopment Corp. has announced that it wants to work with the city to turn an old salvage yard into an “urban forest.” The property has been used in the past as a dump site for various waste products. This project would not only clean up the property, removing old waste, but it would also prevent any further pollution on the property.

These are only two recent examples that I have found of cities working towards a sustainable environment. With groups such as Earth Day Network and the Marian University Science Club working to increase awareness on issues like air and water pollution, conservation, and recycling, hopefully more individuals and communities will start to take steps to go green.

Creationism vs. Evolution: How did we get here? April 30, 2010

Posted by Jill in Evolution, Genetics, History of Science, Science & Culture.
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Darwin's finches

I was in the library this week studying for finals and finishing up the rest of the work in my classes when I came across this book called Is God a Creationist, which contained many valid arguments for both scientific theory as well as theological explanations as to how life on this planet began. The age-old question of our existence has long been debated by both scientists and theologians.

Since Charles Darwin published his findings on the Galapagos finches and his theory about evolution, there has been an intense debate between scientists and theologians. Scientific evidence, such as carbon dating, dates the earth at about 4.54 billion years old, long before the existence of mankind. Theologians argue the biblical implications of the origins of the world saying that Earth was created by God and all living things were created by God. Literal interpretations of the Bible are difficult to comprehend for many reasons including the fact that the Bible was written 3,000 years ago so the interpretation and meaning of words could have been different than what they mean today and the fact that the Bible was not written as or intended to be a historical accurate account of the world because it is a book filled with symbolism.

The Bible contains two creation accounts in the book of Genesis. The first creation account can be found in Genesis 1-11. According to Michael D. Coogan, the first account of Genesis describes the “formation of the cosmos, an ordered universe, out of preexisting but chaotic matter—an unformed earth and unruly sea over which a wind from God swoops like a large bird” (Coogan 28)

The majority of evolutionary theorists believe that there was preexisting matter from which our universe has evolved. Besides the concepts of evolution, scientists are also known for having developed the “Big Bang Theory” to explain the origins of matter in a naturalistic framework, from which our universe was theoretically created. The Big Bang Theory is described as a moment 15 billion years ago when the total amount of matter in the universe exploded from a point and moved out to form the expanding universe today. The scientific perspective on the origins of the world can be described by: “the world had a beginning under conditions in which the known laws of physics are not valid, and as a product of forces or circumstances we cannot discover…the scientist’s pursuit of the past ends in the moment of creation” (Is God a Creationist 35)

Evolution and natural selection cannot be ignored even by theologians because there is significant scientific evidence that states that both do and have existed. At the very least, it is evident that at least artificial selection exists because of the domestication of animals such as horses, dogs, and cats. Humans were able to domesticate or breed certain characteristics of an animal, for example wolves that were friendlier to man than those that tried to attack, and cultivated these characteristics over thousands of years to produce the species we know as our four-legged friends, dogs.

Do chimps think and act like us because they are one of our closest ancestors?

Through molecular genetics, it is possible to find evolutionary pathways through the similarities in homology of DNA between different living species. Also, extracted DNA from fossilization records are the scientific equivalent of “paternity tests” of our earliest ancestors, determining how closely related we are genetically to other species, namely apes. Molecular geneticists as well as evolutionary theorists believe that chimpanzees and humans emerged from a common ancestor 6 million years ago, dating long before the creation of Adam and Eve (according to the Biblical timeline). The genetic evidence for humans being potential “cousins” of chimps is astounding in that approximately 99% of our DNA is identical to that of chimpanzees. The one percent variance between our DNA and that of chimpanzee DNA is what distinguishes us from apes, but in the genetic world one percent could potentially mean that all of the DNA in that one percent is what makes us distinctly different from say starfish. Although theologians refuse to believe that humans evolved from apes, how do we account for species such as the Geico Neanderthals or other upright-walking mammals that shared more behaviors with humans than chimpanzees do. Neanderthals looked more like humans today than modern apes do, so how does religion account for these differences?

An interesting view on the culmination of both the scientific and religious aspects concerning our existence can best be described by John MacArthur: “For the scientist who has lived by his faith in the power of reason, the story ends like a bad dream. He has scaled the mountains of ignorance; he is about to conquer the highest peak; as he pulls himself over the final rock, he is greeted by a band of theologians who have been sitting there for centuries.”

The PCR song April 29, 2010

Posted by Dr. O in Biology, Fun, Genetics, Science & Culture, Science Education.
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To build on the post containing the rap song on photosynthesis, I thought I’d add this little music video montage put out by Bio-Rad. It’s hilarious.  See…scientists DO have a sense of humor.

Here is the original Bio-Rad link.

Bacteriophages have been found to have new uses–making car fuel! April 29, 2010

Posted by Jill in Biology, Chemistry, Environment/Conservation, Fun, Genetics, Science & Culture.
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hydrogen-fueled car

For those molecular geneticists out there, you will appreciate the new discovery of using a genetically modified M13 phage as a source for making hydrogen fuel out of water!

The M13 bacteriophage is often used in molecular genetics work as a cloning vector. The phage contains a single strand circular DNA genome of 6407 nucleotides that is released into a host cell as a result of the phage absorption. When used in a host cell, the, the host cell proteins will form the double-strand replicative form (RF). This new circular RF DNA is required for M13 packaging because the viral proteins are synthesized from mRNA transcribed off the strand of the RF molecule. From here, M13 DNA is packaged at the host cell membrane, and then releases the infectious particles.

Researchers have found a way to harness the M13 virus in such a way to break apart water molecules, producing hydrogen fuel. Researchers have been able to genetically modify the M13 virus, normally infecting bacteria, so that it would instead bind to a catalyst called iridium oxide and a biological pigment, zinc porphyrins. The viruses then will naturally arrange themselves into a wirelike structure while the catalyst and pigments will harvest sunlight to divide the oxygen from the water molecule. The virus works in this mechanism in that the pigment acts as an “antenna” to collect the sunlight and transfer the energy down to the virus, emulating photosynthesis.

Researchers have successfully been able to separate the oxygen from the water molecule, which is the hardest part of the water-splitting process. The hydrogen will then split into its parts (electrons and protons), but researchers are still attempting to harvest the hydrogen parts in order to collect the gas separately and then convert the gas eventually into hydrogen fuel.

The benefits to this are numerous, including finding a green way of obtaining hydrogen fuel without creating carbon emissions as well as making the process self-sustaining. The ability to harness the mechanisms of photosynthesis in order to control the electron transport in a system is one of the biggest problems in creating a system for artificial synthesis, but this approach allows the transfer of electrons to be controlled.

The full article can be found here: GM viruses offer hope of future where energy is unlimited

I have also included an entertaining rap dealing with photosynthesis: Photosynthesis Rap

And before you’re a skeptic and are thinking that no one would make up a rap about photosynthesis, I found another rap about ATP synthesis: ATP Synthesis Rap

A Different Kind of Canary April 28, 2010

Posted by ecogeeko10 in Ecology, Environment/Conservation, Genetics.
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timber rattlesnake

What’s the difference between a canary and a timber rattlesnake? Not much if you’re a conservation biologist who is examining the effects of habitat fragmentation on biodiversity.

A recent study by a group of Cornell University researchers shows that even some of the simplest forms of human disturbances are having large impacts on biodiversity. Timber rattlesnakes in particular, have been a major focus in the northeastern region of the U.S. because these scientists have been able to utilize fine-scale molecular genetics and microsatellite markers to track the rattlesnake populations. They are finding that fragmentation caused by small scale road development is having a more than noticeable effect on the genetic diversity of these snakes. For this reason, one could compare the rattlesnakes in this study to canaries in a coal mine.

Of the 500 individual snakes taken from four separate regions and 19 hibernacula, none of the genetic clusters spanned either major or minor roads. This greatly proves to the non-believers that roads are indeed significant barriers that limit the dispersal and other natural processes necessary for species survival. Don’t assume, though, that this is only affecting the timber rattlesnake populations. Countless other studies show that habitat fragmentation is causing the demise of many of our planet’s species. Nevertheless, this study is unique because it only deals with roads. When people think of habitat fragmentation, they usually think of rainforest deforestation or mountaintop removal—they don’t always realize that something as common as a road can be quite detrimental to a species. Hopefully this study will help us to learn to notice the “smaller things” that can hurt the environment and maybe we can be inspired to do something about it.

The Song of the Dodo

Before I end this blog, I just wanted to mention that there are a few books that I hope to read this summer, including a book called The Song of the Dodo: Island Biogeography in the Age of Extinction, by David Quammen. This greatly relates to this recent study that was done with timber rattlesnakes because it talks about habitat fragmentation and its implications on biodiversity. I am hoping to learn something from this book and I was also thinking that it would be cool if others read it too. Perhaps we could even discuss our thought of the book at the end of the summer (via the MU Blog)! I am also willing to take other book suggestions—it could be like an “online summer book club” or something. Let me know what you think!

Pollution is Good? April 28, 2010

Posted by Colleen in Climate Change, Environment/Conservation, Health, Policy.
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Marian University celebrated Earth Week  last week (April 19th-22nd). We even hosted an outdoor movie and taught everyone the importance of recycling!  That same week the EPA put out a report saying that air pollution has dramatically reduced over the past twenty years. To me, that seems like a really good thing, but according to a recent NPR story, clean air could actually be intensifying global warming.

Shocked?  Me too.

But, according to science writer Eli Kintisch, this could be the case.

Why is this so?

Well, there are two kinds of air pollutants: aerosols and greenhouse gases. Greenhouse gases warm the planet, which we are well aware of, but recently scientists have discovered that aerosols actually have a temperature maintaining effect for the earth. Apparently if all man-made air pollution was stopped, global warming could be sped up by as much as a degree Fahrenheit. While greenhouse gases absorb heat, adding to global warming, aerosols actually reflect sunlight away from the earth causing the earth to cool down rather than heat up. By cleaning the air, we’re taking away this stuff away, perhaps adding to the increase in the global temperature. These pollutants still cause health problems, like asthma and respiratory disease, so letting them stay in the atmosphere isn’t necessarily the answer. The scary thing is that we don’t know how much these cooling effects have slowed down global warming. If it’s a lot, then taking the aerosols away could cause a huge problem. This would mean that we’ve been causing a larger warming effect than we originally thought. If not, then it may not be as much of a concern.

One idea that has come about from this knowledge is to use geothermal engineering to fix the problem caused by removing these cooling pollutants. What we would do is inject new pollutants into the clouds, allowing for the cooling to occur. Theses sulfur aerosols are distributed naturally during volcanic eruptions, such as the one we’ve been seeing in Iceland. Volcanoes, when they erupt, put out a lot of sulfur aerosols  into the stratosphere and can cause cooling to happen. The idea is that if there is a natural emergency in the future caused by the warming, it might be possible to slow or stop the warming by mimicking the volcanoes and injecting these aerosols into the stratosphere.

Crazy huh?

To hear the whole story, click here.

Is it a good or bad time for students who dream of going to medical school? April 28, 2010

Posted by Jill in Health, Medicine, Policy.
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With the passing of the 2010 healthcare bill, many more Americans will have access to healthcare.  Prior to the bill many people were unable to afford the astronomical costs of seeing a doctor regularly, not to mention paying for surgery or major medical procedures without insurance.

For many aspiring medical students, this is great!

There will be a need for more physicians to accommodate the number of patients that will be receiving this affordable healthcare. The need for primary care physicians is expected to skyrocket based off of the sheer number of physicians needed to meet the demand of a growing number of potential patients.

Where do we get these primary care physicians?

The problem that arises with the growing need of primary care physicians is that so many medical school students want to specialize in a particular field of medicine such as surgery or  cardiology because they have a particular passion for their interest. Also, physicians that specialize have a significantly higher income than those who are primary care physicians. Today, the United States is already shorthanded when it comes to primary care physicians and it will be difficult to meet the needs of the growing number of patients as they receive greater healthcare benefits.

There are some medical schools in the United States such as the University of Colorado School of Medicine and Rocky Vista University College of Osteopathic Medicine that are responding to this call for primary care physicians by encouraging their students to get into primary-care medicine, such as pediatrics, OB-GYN, internal medicine, and family practice. With the annually increasing cost of medical school, it is difficult to steer students away from high-paying specialties. The University of Colorado, along with other medical schools, has started a “pipeline” program which allows promising high school students direct admission to medical school following college and help them with their debt, so as to encourage students to defer the cost of medical school. Also, increasing the size of medical school classes has helped in graduating more physicians per year, which will help in meeting the soon high demands of patient care.

How do we encourage students to be  primary care physicians?

Because the cost of medical school is so high, more programs need to be implemented to help medical students pay for their medical school and not have to rely on specializing in order to repay med school loans. The benefit of going to medical school at this point is that the job market isn’t saturated in the field for primary care physicians, but the question remains, who is willing to take the pay cut and potentially lengthen the amount of time it will take to pay off the debts of medical school?

If our government is willing to provide insurance to those who could not before afford it, should our government also be responsible for helping medical students with their tuition costs in order to provide these new patients with the proper healthcare that our country is known for as well as the manpower to manage the number of new insured patients?

A Second “Lab Rat” has its Genome Mapped April 28, 2010

Posted by ecogeeko10 in Behavior, Biology, Evolution, Genetics, Health, Neuroscience, Physiology.
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Many behavioral ecologists, geneticists, physiologists, etc. are familiar with the zebra finch (Taeniopygia guttata). In fact, many have considered it to be the avian version of the white lab rat. Because of this, these researchers should be excited to hear that scientists have just recently decoded the zebra finch’s genome.

A genome to explore behavior

The zebra finch isn’t the only bird to have its genome mapped (the chicken was completed first) and it’s only about one-third the size of the human genome. However, this was a unique find because it will greatly help behavioral ecologists to understand the underlying mechanisms that help baby songbirds learn how to sing from their parents. This isn’t something that could have been done with the chicken genome because chickens don’t learn how to “cluck” from their parents—they just do it. Zebra finches, on the other hand, are similar to humans because human children also learn how to speak from their parents.

The zebra finch genome gives us the opportunity to explore the influence of genetics on language development.

Researchers are already analyzing the genome and they are finding that a good portion of the bird’s DNA is actively participating in the hearing and singing of songs. What’s more, these short simple songs are rooted in a great deal of genetic complexity. To date, it has been understood that the very act of singing and hearing songs activates large, complex gene networks in the bird’s brain. However, the current genomic research is revealing there to be many more participating genes than once thought. Right now it seems that there may be approximately 800 total genes that are active in this process!

Genes not acting as genes

New evidence is also showing that many of the activated genes aren’t acting like genes in the traditional sense. Rather than coding for proteins, the DNA from these genes is transcribed into short stretches of non-coding RNA that control the expression of other genes involved in the zebra finch’s vocal communication. Since non-coding RNAs are very influential in the developmental processes in animals and since they are thought to be instrumental in the evolution of higher organisms, the vocal learning that is found in the higher organisms may use non-coding RNAs as their driving force.

The evolution of language

It is also worth noting that when comparing the newly mapped zebra finch genome with the chicken genome, there seems to be some obvious differences that may point towards the evolutionary pathway that gave rise to birds that are capable of vocal learning. For instance, the evolution of the ion channel genes—which are important players in behavior and neurological function—in the zebra finch brain were greatly accelerated; the expression of the male sex chromosome genes seems to have been modified; and the production of new variants of neurobiologically important genes have taken place. It is amazing to see how much has learned in such a short period of time!

From birds to humans

It took the combined effort of more than 20 institutions to map out the genome of this song bird and now everyone has the opportunity to reap the benefits from this work. The newly gathered information should prove to be instrumental in helping us to better understand how humans learn language and perhaps it will help neuroscientists to identify the genetic and molecular causes of certain speech disorders that are associated with various illnesses such as Parkinson’s disease, strokeautism, etc. With the parrot genome scheduled to be completed by the end of this year, who knows what all we can learn about our little feathered friends and even ourselves!