Science Friday: DNA Testing

We’re very excited to bring you this weekly feature – Science Friday, a science talk show produced by NPR. Each week, a new video takes on a different on science topic, in an effort to bring an educated, balanced discussion to bear on the scientific issues at hand.

You may remember that we started this feature more than a year ago – but technical difficulties kept us from making it a regular appearance. Thanks to the fine folks at SciFri, however- I think we’ve got it figured out. Hopefully, we’ll be bringing you the science-y goodness every Friday from now on.

This week we follow two high school students from New York as they perform a DNA test on foods to see just what ingredients are in our everyday meals. They review if goat milk really comes from goats, the origin of caviar, and what exactly goes into New York City hot dogs.

Can’t see the video? Click here to view it.

The Eyes Have It: Evolutionary Development and DNA

Today’s guest blogger is Neal Immega. He has a Ph.D. in Paleontology and is a Master Docent here at HMNS. In his post below – originally printed in the Museum’s volunteer newsletter – Neal discusses Evolution Development and DNA.

Popular media crime shows, like CSI: Crime Scene Investigation, show amazing applications of DNA technology. For example, a person can be traced to a specific location by means of cells he left on a door knob.

A new science called “Evo-Devo,” shorthand for Evolutionary Development, can tell us even more amazing information. Evo-Devo techniques probe deeply into the structures of DNA to look at how DNA actually codes for the growth of body parts, telling us more about the animal kingdom than we ever dreamed possible. It shows genetic similarities between very different organisms and lets us understand how two organisms, like mice and men, can have DNA that is 85% similar and, yet, code for very different organisms.

We all know the basics of DNA molecules, where the genetic code is stored by a very long sequence of four proteins strung together in various arrangements. That is the easy part! What we need to
worry about is how these genes blueprint a living being. Geneticists, like Sean Carroll (whose popular books are listed in the references box), have discovered that the DNA code is made up of some large master programs that control things, such as eyes, and lots of very small programs (they call them switches) that control what kind of eye will be displayed.

Normal Fruit Fly
Image courtesy of The Exploratorium

Let’s confine ourselves to understanding and experimenting on simple life forms, such as fruit flies. To figure out which specific piece of DNA causes some feature to appear in a developing embryo, geneticists experimentally inactivate a segment of DNA, transplant the complete strand (including the inactivated segment) back into the egg, fertilize that egg, and then see what turns up missing. If that missing part is not vital for survival, the egg might even grow into an adult fly. Compare the drawings of a normal fly with the one below it where the master program for eyes has been deleted.

Eyeless Fruit Fly 
Image courtesy of The Exploratorium

Such experiments have found that the master program for making eyes can cause an eye to grow on a fly’s leg, body, antenna, or inside the body, depending on where it is placed on the DNA strand. Check out the drawing showing the results of moving the master program for legs to the site of the antenna. Note that the extra legs are fully formed but lack the neuron connections to the brain and so are not functional. (In the references box is a link to an electron microscope image of a real fruit fly that shows a mutation in which eyes replace antennae.)

Various mollusks (like clams, snails, and octopuses) grow eyes that vary in complexity from very simple sensitive pits to complex eyes that would compete well with human eyes. The EXACT SAME eye master program from a fruit fly can replace the eye master program for a squid, and it will grow a perfectly functional squid eye. You might be tempted to say that fruit flies and squids are cousins.

Fruit fly with extra legs
replacing the antennae 
Image courtesy of The Exploratorium

That is an amazing statement, but to take it even further, the same experiment with a mouse eye master program will grow fly eyes on flies and squid eyes on squids. They only differ by the small switch segments. These experiments establish a link between vertebrates and invertebrates that paleontologists are unlikely to find in the rock record. This also helps explain the amazing degree of structural similarity between mice and men—although many of the master programs are similar, the really critical parts of the DNA are the small switches that control the details.

Mollusks have just one master program that is controlled by different switches. Pectens, for example, have the most complex vision arrangement of any animal with three different types of eyes on its body. The DNA can be experimentally adjusted to grow any of these eyes anywhere on the body. Random mutations could thus cause novel arrangements, and survival would judge their fitness—evolution in action.

The switch concept explains how mice, chimps, and humans can have a similar number of genes. The switches control the result of the master programs. You can pick up any modern textbook and read that men and chimps have nearly identical genes. It is the switches that make us different and that provide the evolutionary means for dramatic changes, good and bad.

The fossil record is full of cases where a dramatic new species just appears. Paleontologists have often wondered if this was caused by a missing rock interval, by migration, or by rapid evolution. The concept of rapid evolution has often been discounted because it seemed to violate the incremental nature of evolution. We now can see how rapid evolution may just be a single point mutation in a switch. There are numerous biological examples where altering one protein is lethal, as in Tay-Sachs disease, or altering another might bear strongly on survival, as in changing
the color of hair from white to black.

Geneticists can now explain things in a way that profoundly affects how we think about evolution. Biologists and paleontologists have always wondered if evolution had to generate complex structures like eyes from scratch for each phylum. The reuse of master programs from very simple life forms through complex ones means that evolution can build on what went on
before. Critics of evolution often claim that eyes are too complex to have evolved. (The “half-an-eye-is-nogood” argument is derived from the first sentence of the Darwin quote in the box below.) Now, with Evo-Devo tools, we can see commonalities between the genetics of simple life forms and complex life forms– between clams and people.

The possibilities just became more complex.

REFERENCES:
Wyoming Dinosaur Center: http://www.wyodino.org/

Sean B. Carroll:
Endless Forms Most Beautiful: The New Science of Evo-Devo, (paperback) 2006
The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution,
(paperback) 2007
Remarkable Creatures: Epic Adventures in the Search for the Origins of Species, 2009

Lynn Helena Caporale:
Darwin in the Genome: Molecular Strategies in Biological Evolution, 2002

SEM (scanning electron microscope) photograph of eyes replacing antenna in a fruit fly by Naoum
Salame. http://1tv4.sl.pt

Fly Eye Genetics:
http://www.pbs.org/wgbh/evolution/library/04/4/text_pop/l_044_01.html
Renowned scientist Dr. Walter Gehring discusses master control genes and the evolution 
of the eye.

Darwin, 1859, The Origin of Species, http://darwin-online.org.uk/contents.html. In most editions, the quote appears on pp143-4.

We’ll, I’ll be a Monkey’s Uncle. Or an Orangutan’s.

Our Guest blogger today is Dr. Todd Disotell, a professor of anthropology and a molecular primatologist at New York University’s Center for the Study of Human Origins. He will be speaking at HMNS on Feb. 9 at 6:30 p.m. about new molecular analytical techniques and how mapping whole genome sequences has affected what we know about the past. In his blog below, Dr. Disotell debates a recently proposed theory that humans are more closely related to orangutans than chimpanzees – a theory he disagrees with.

Posing for the Camera
Creative Commons License photo credit: jimbowen0306

This past summer upon the publication of a paper by a colleague, I found myself at the intersection of a 25 year old hypothesis, the latest research in genomics and bioinformatics, and popular culture.  Jeffrey Schwartz of the University of Pittsburgh and his coauthor, John Grehan of the Buffalo Museum of Science published an updated version of their hypothesis that orangutans are more closely related to humans than are chimpanzees in the Journal of Biogeography.  This intrigued me because in my final year of graduate school, my advisors and I published one of the earliest papers utilizing DNA sequence data supporting the growing consensus that chimpanzees were our closest relative, followed by gorillas, and much more distantly orangutans.

Perhaps due to my working in New York City, a producer from the Daily Show with Jon Stewart called me at my office and wanted to know if I was willing to be interviewed about Schwartz’s hypothesis.  As a fan I readily agreed and correspondent John Oliver was dispatched to my laboratory to interview me.  During the course of the interview in which I stated that the hypothesis flew in the face of all known genetic evidence, I opined that I would at least get to write a counter paper and perhaps a counter-counter paper if Schwartz responded.  That got me thinking about newly available genomic data that was now available in various databases which had not been fully analyzed.

Confused chimp
Creative Commons License photo credit:
Tambako the Jaguar

I then downloaded the complete genome alignments that included human, chimpanzee, gorilla, orangutan, macaque, marmoset, lemur, and galago.  After writing a series of Python scripts (an open source computer programming language) to parse and reformat the masses of sequence data, I chose the first 1 million bases of each chromosome for which all of the above species were represented.  I then used well characterized statistical and analytical techniques to infer the evolutionary history of each DNA region.  Not surprising to me, the analysis of each region convincingly rejects the hypothesis that orangutans are more closely related to humans than are chimpanzees.  Furthermore, when these 30 million DNA bases are used to estimate the time of divergence between humans, chimpanzees, and orangutans using molecular clock techniques, the orangutan appears to have diverged at over twice the age chimpanzees have from humans.

These results are not at all surprising to the absolute majority of paleoanthropologists and evolutionary primatologists.  However, it is still worthwhile to occasionally revisit theories and hypotheses that we now take for granted when new data are generated and new analytical techniques are developed.  In this genomic age, as the genomes of more and more species and even individuals within species are being sequenced, a whole new class and scale of analyses can be carried out from the keyboard.

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Check out Dr. Disotell’s lecture, “Times Are a-Changin': New Methods Tell A New Tale of Primate Evolution” at HMNS on Feb. 9 – get tickets here!

Genetics and Archaeology: Helping Us Understand the Past

Recently I came across several examples of how genetic information has greatly helped us understand the past. Quite often this data is gathered in the most unexpected places. Consider these examples.

In an article published in December 2009, an international group of scientists addresses the issue of the extinction of North American megafauna traditionally dated some 11,000 years ago. A skeleton of a woolly mammoth on display in a museum never fails to impress us. At the same time, most of us would agree that it is a good thing we don’t have to worry any more about these lumbering giants messing up our evening commute. However, what most of us stop worrying about is when these animals became extinct and why. Most of us, that is, but not all of us. This is where the story of ancient DNA retrieved from perennially frozen soil comes in.

A traditional approach to estimate when and where a species became extinct has been to map and date the last known survivors. The thinking was that knowing when and where the last specimens lived would automatically clue us in as to why they died out. Is this true, however? Do these last known survivors really represent that last ones left standing? Or did we miss them and make wrong assumptions?

Creative Commons License photo credit: rpongsaj

The party line about woolly mammoths was that they survived on remote islands in the far northern regions of Alaska and Siberia, a region referred to as Beringia. That is now old hat. New genetic data tells us a different story. Mammoths may have survived much longer than originally thought in the Alaskan interior. Scratch 13,000 years ago. Now it looks like woolly mammoths may have survived for an additional 2,600 to 3,700 years in parts of Alaska. Mitochondrial DNA was retrieved from perennially frozen soil near Stevens Village in the Yukon Flat. What we have here then is a suggestion that we can establish the presence of certain animals in a region at a certain time in the past. No bones needed. Just animal DNA left behind in the soil and preserved because of the permanent frozen condition of the dirt.

While the researchers were careful to address any shortcomings of their approach (contamination of the soil, migration of more ancient DNA from lower-lying areas to more recent layers closer to the surface), there will be reactions from other members in the scientific community. This may be frustrating to those among us who like to see “the final answer” to questions like these, this dialogue is part of what science is all about. We will have to see if these new results will stand up to the criticism that will come.

As megafauna slowly disappeared from the North American landscape, human settlers were making their presence felt. I have written about the questions of where these earlier migrants into the Americas may have come from. There is very good evidence that the Paleoindians migrated from parts of Asia.

Research into a disease known as multifocal leukoencephalopathy resulted in the discovery of a virus labeled as the “JC virus.”

It turns out that we all have a copy of this virus residing within us. It is harmless to most of us, unless your immune system is compromised. Geneticists studying this virus found that it was remarkably stable and very rarely mutated into a new variety. Moreover, the strain of the JC virus carried by the Navajo today is nearly identical to that carried by the modern inhabitants of Tokyo. The JC virus bolsters an Asian origin theory for the First Americans.

Beringia – Image courtesy of NASA.

As to how Paleoindians arrived into the Americas, genetics can help us focus that picture as well. If one accepts that the Bering Strait was an ancient migration route – and most people have no problem accepting this – then the issue is: exactly what route did they follow? A coastal route and an interior, overland route, often suggested by archaeologists, now both seem to have been used.

North American mitochondrial DNA, collected from contemporary populations, points to two migration routes. In a paper published Jan. 19, 2009, scientists studied various mitochondrial DNA haplogroups, zooming in on two rare groups. One of these (known as D4h3) is found only along the Pacific coast and is mostly in South America, while the second group (X2a) is restricted to northern North America.

The presence of X2a in North America east of the Rocky Mountains may support the idea of an ice-free corridor between two ice sheets covering Canada and parts of the US. Some of the earliest migrants may have followed that route which would have taken them into the Great Plains, where the glacial corridor would have ended. The presence of D4h3 along the Pacific may represent a coastal migration route.

Woolly mammoths leaving their DNA in the soil, viruses carried by all of us and DNA shared through the mother’s family line all help us refine and refute some of the ideas on how the first immigrants arrived in the Americas. I am sure genetics will continue to add to our understanding of this momentous period in human history. Stay tuned.