QUEST Community Science Blog Author: Dr. Barry Starr

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5 out of 9 Justices Recommend Leaving Innocent People in Jail

June 22nd, 2009 by Dr. Barry Starr

In a truly awful decision reminiscent of Gore vs. Bush, the Supreme Court has decided that there should be no federal mandate for genetic testing after someone has been convicted. Even though DNA evidence can free innocent people who were wrongfully accused. How absurd is this?

It is especially hard to understand when there is ample evidence that there are plenty of innocents in prison. And when a DNA test can prove so conclusive in showing their innocence.

A case I use in a high school activity (and which will be highlighted in the new Technology Benefiting Humanity exhibition at The Tech) involves Marvin Anderson. He is an African American who was convicted of rape by an all white jury in the South.

Court TV produced a great documentary that details all of the mistakes that sent Marvin to prison. And how the Virginia state government, much like our current Supreme Court, fought the simple DNA test that eventually proved his innocence.

Marvin was a suspect because he had a white girlfriend and the rapist had said that he had a white girlfriend during the attack. In a photo line up, Marvin’s was the only picture in color. Then, in the real line up, Marvin was the only man who had been shown in the photo line up.

Marvin’s lawyer represented the man who had really committed the crime. The trial lasted one day and as I said, Marvin was sent to jail by an all white jury. And while Marvin languished in prison, the real rapist confessed but the judge threw out the confession.

This is when the Innocence Project took up the case. The Innocence Project uses genetic testing to free innocent men and women. After hearing the details of Marvin’s case, they decided to help him clear his name. And it was not easy!

First off, they had to find the evidence from the case. This is often hard to do because evidence gets thrown away after a certain amount of time.

But, by a miraculous fluke, the Virginia government found the evidence from the rape kit… it had been saved in a lab notebook. So all that needed to be done was to see if the DNA from the crime scene matched Marvin's. If it didn’t, then Marvin most likely was innocent.

But the Virginia government would not allow the evidence to be tested. Apparently, just like the Supreme Court, procedure mattered more than innocence to the bureaucrats involved.

How many people like Marvin Anderson are waiting for the justice system to do the right thing?
Finally, in 2001, after Marvin had been in jail for 15 years and spent four years on parole, Virginia passed an Innocence Project backed statute that allowed DNA evidence to be tested in some cases. Marvin’s was the first evidence tested under the new statute. He was found to be innocent and the police were able to use the evidence to catch the real rapist.

If the Virginia government had not done the right thing, the real rapist would be free to continue committing crimes. And everyone would still see Marvin as a rapist.

There are undoubtedly Marvins rotting in jail in the three states that don’t allow for genetic testing after a conviction (Alaska, Oklahoma, and Massachusetts). And other Marvins are probably in those other states that only allow genetic testing in certain situations.

The Supreme Court could have given all of these innocent people the chance that Marvin finally got after 19 years. But five justices decided against doing that.

Now I suppose there is probably some legalese reason why the Supreme Court ruled that innocent people should stay locked up. But I am not lawyer enough to understand it. And neither are the Marvins still out there, waiting for justice.




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Posted in KQED | 3 Comments

Using Mice to Understand Human Speech

June 8th, 2009 by Dr. Barry Starr

It will probably take more than a human FOXP2 gene to reach this future.Scientists have started to look at DNA to try to figure out why we can speak and other animals can't.  One gene that has caught their attention is called FOXP2.

People with a certain version of this gene have trouble forming words and speaking but are otherwise OK.  This is exactly what you would expect if a gene were primarily involved in speech.

One way to test this idea would be to put the human version of the gene into an animal and see what happens to that animal's speech.  A natural candidate would be the chimpanzee.  Humans and chimps are around 98.8% similar at the DNA level* and their FOXP2 gene has only two differences.

Unfortunately (or fortunately…), we can't yet do this experiment because we aren't very good at changing a chimp's genes.  But what we are good at is changing a mouse's gene.  And this is exactly what scientists did in a new study.

The scientists changed a mouse's FOXP2 gene into a human's.  Now no one expected that we'd have a Mickey Mouse on our hands.  Mice just don't have all the equipment for speech and it is really unlikely that the only difference between mice and people in terms of speech is this gene.

But by putting a human FOXP2 gene in mice, we can learn some things about how the gene influences human speech.  Does it change the vocalization part of the brain?  Does it change something with mouth anatomy?  Something with breathing?

The results with these mice were interesting.  They weren't suddenly chatty but changing the gene definitely caused the mice to emit different squeaks than their natural cousins.  The vocalization part of the mouse's brain also changed.

These results suggest that FOXP2 affects human speech at least partly through changes in the brain.  And that if you give a mouse a human Foxp2 gene, you change the way it communicates.

The next steps are a little harder to figure out.  We do know that Neanderthals had the same FOXP2 gene that we do.  Perhaps by comparing human, chimp and Neanderthal DNA we'll be able to find other genes involved in speech too.  We'll have to wait a few months for this kind of analysis as the Neanderthal genome isn't quite done yet.

*When we include extra copies of some DNA and missing DNA, the similarity goes down to 96%.

Here is a video discussing the results of the study.




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Penny Wise, Science Foolish

May 26th, 2009 by Dr. Barry Starr

Kids will want to keep learning science when they see how fun it is.The economy is in the tank and so the cuts at schools begin. And of course one of the first things on the chopping block is anything that can keep kids interested in science.

These programs tend to be more expensive than other programs and so are natural targets for the axe.  For example, at my kids' school, they are cutting 5^th grade science camp.

Kids go off for a 5 day trip to a place out in the woods to study nature.  The kids have a blast and can see that science is more than memorizing phyla or sedimentary, igneous and metamorphic rocks.  Instead they get to explore nature and use books to figure out what they're seeing.

And if history is any guide, there will be a big fall off in field trips to zoos and museums too.  These are more places where kids can see that science is actually a lot of fun.

Some might argue that if money is limited these programs should be cut.  This is true only if we want a workforce that can't do the jobs that are becoming available in our information based economy.

To do well in the future job market, people are going to need a good basic understanding of science and/or engineering.  Think about what an auto mechanic does these days.  Or a nurse or a radiologist.

We need to keep people studying science for their own good.  And frankly, for the good of the U.S. as well.

One of the keys to getting more people to take the science they need is to show them how fun and exciting it is.  We need to let them see that science is actually about studying the mysteries of the natural world and applying them to make that world a better place.

This is what the programs that are going to be cut do.  Without them, schools will continue to turn kids away from science.  And the U.S. will fall behind other countries.

I have no idea what programs should be cut instead and I am sure that other people see higher priorities than science camp.  But I think it is time that public schools recognized that science is as important to a student's future as are the three R's.  Someone needs to come up with a way to make science into an R so we can have the four R's.  Any ideas?




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Posted in Education, Partners | Please Comment

Fearing 1918

May 11th, 2009 by Dr. Barry Starr

Animal viruses can be more deadly than their human
counterparts
A lot of people have been commenting about the apparent overreaction of governments to the swine flu.  Why go to such extreme measures to deal with simple influenza?  The reason has to do with the flu pandemic of 1918-1919.

Over those two years, at least three waves of flu struck killing over 600,000 people in the U.S. and a staggering 30-50 million people worldwide.  People died at such a high rate that cities ran out of caskets and dead bodies were stacked on porches and in the streets.

Governments have been concerned that history might repeat itself because the two flues share one thing in common–they both started out as animal viruses.  And our bodies are not particularly good at fighting off viruses new to humans.

Each year a new flock of flu strains kicks off the flu season.  Almost always these strains are variations of human flues from previous years.  What this means is that we have seen cousins of these viruses in the past and so have a leg up on mounting an attack and defeating them.

We do not have this same leg up on animal viruses.  Our immune systems haven't seen anything like them and so can't mount a quick attack.  The end result is that the percentage of people who die from animal flues tends to be much higher than from run of the mill human flues.

In any flu season, the CDC estimates that 5-20% of the U.S. population ends up with the flu.  And that 36,000 of these people die.  The numbers of deaths would be much higher if a truly deadly animal flu virus like the bird flu from a few years back were to emerge and gain the ability to spread from person to person.  (The bird flu was never more than a few isolated cases since it never gained this ability.)

At first blush, this is what the swine flu looked like.  The disease spread easily among people and, in Mexico at least, appeared to be more deadly than normal flues.  So governments around the world sprang into action.  Since flu is spread through contact, governments tried to keep people away from each other.

They closed schools at the fist sign of trouble.  Mexico closed restaurants, theaters and museums too.  All of this was done in an attempt to prevent the spread of a disease like the flu of 1918.

At least outside of Mexico, this flu does not seem to be too much worse than other flues.  So it may be that governments overreacted this time.  But I would prefer that they overreact like this as opposed to ignoring a deadly pandemic.  We don't want another 1918 on our hands.

More info on The 1918 Flu in San Francisco




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Tracking Genetics in Popular Culture

April 27th, 2009 by Dr. Barry Starr

Shows like CSI can increase the public's awareness of geneticsOne of the most fun parts about my job is answering people's genetics questions at our Understanding Genetics website.  We get around 200 questions each month from all over the world and they definitely keep me on my toes.

They also give me a feel for what is going on with science in popular culture.  I can tell this by looking at Google Analytics data and seeing which of our previous answers has had an upsurge in visits.  (We post around one new answer online per week.)

For example, whenever PBS airs a show on how a mutation called CCR5-delta 32 may have made people resistant to the plague, I get an uptick in the hits on the answer that deals with that topic.  When House (a show on Fox) had a character say that of course someone was adopted because he had a cleft chin and his parents didn't, I got an uptick on the Chimeras start out as fraternal twins that fuse together at a very early stage.  What this means is that chimeras have two sets of DNA.  Some of their cells have the DNA from one twin and the rest of their cells have DNA from the other twin.

As you can imagine, these folks can wreak havoc with a police investigation!  What happened in the CSI episode was that the DNA from the crime scene did not match the DNA from the most likely suspect.  In the end we find out that the suspect is a chimera and that the evidence left behind at the crime scene had one set of DNA and that the blood they tested had a different set of DNA.  From the same person!

It is great that there is so much science starting to seep into popular culture.  If the science is accurate, it is a great way to get people involved in science.  I just wish it was accurate more often.




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Designer Babies

March 30th, 2009 by Dr. Barry Starr

Credit: Deutsches Bundesarchiv (German Federal Archive)
A storm of protest broke out a month or so ago when a fertility clinic in Los Angeles announced it would start helping women choose what their babies might look like. The ruckus was loud enough that the clinic has since backed off on this service.

And this is probably a good thing. I am not sure this is a road we want to go down– it smacks a bit too much of Hitler and a perfect race.

Of course, we've started down this road a ways already. We aren't able to shape anyone's DNA yet. We don't have the technology to do this in any safe or reliable way and frankly, it'll probably be a long time before we can.

But we can take a peek at an embryo's DNA if the egg has been fertilized outside of the body. The process is called preimplantation genetic diagnosis or PGD. Using PGD, scientists can look through a number of embryos' DNA and pick the one(s) the parents want.

Right now we can't scan all of an embryo's DNA. We have to pick and choose what part of the DNA to look at.

For example, PGD is often used to make sure that an embryo has all 46 chromosomes. This service increases the chances for a successful birth for women who are going through repeated miscarriages.

Of course, if we can look at the chromosomes, we can also tell whether the embryo is a boy or a girl. Often this is done to select for girls in families that carry male specific genetic diseases like Duchenne muscular dystrophy. But it is also done for the less life threatening goal of an even number of boys and girls in a family (gender balancing).

PGD can also be used to make sure an embryo did not inherit specific diseases like cystic fibrosis or sickle cell anemia that might run in the parents' families. These diseases can be screened for by looking for specific DNA differences in certain genes. Which is what this fertility clinic wanted to do for hair, skin and eye color genes.

Let's say a parent wants a redhead with brown eyes. The clinic would screen for certain versions of the HERC2 gene that mean brown eyes and certain versions of the MC1R gene that indicate red hair. When they found an embryo with the right combination of traits, then that embryo would be selected for implantation.

Remember, the people at the clinic can't change the DNA of the embryo. They can only sort through the genes that are already in the pool. So if one parent doesn't carry a red hair version of MC1R, then the parents can't have a red haired child.

Even without this ability, the furor over the fertility clinic's service raises a very important discussion point– where do we draw the line with PGD? And who should draw that line?

Obviously eye color is going too far (or is it?) and preventing an early death from a genetic disease is OK. But is it OK to look at gender for family balancing? This is allowed in the U.S. right now but is not permitted in most other countries.

What about conditions like high cholesterol? Or diseases that kill later in life like Huntington’s disease? Or traits like height, weight, or intelligence? Who gets to decide?




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Why Human Cloning Shouldn't be a Big Worry

March 16th, 2009 by Dr. Barry Starr

Identical twins are more similar to one another than a clone
will be to the person cloned.President Obama lifted the ban on federal funding of embryonic stem cell research last Monday. Many researchers breathed a sigh of relief as they could finally get to work using these cells to find treatments and even cures for many debilitating diseases and injuries.

Of course, these cells aren't any less controversial than they were eight years ago. Researchers will still need to destroy embryos to get these cells (at least until they perfect iPS cells which would make this part of the debate moot). Anyone who considers an embryo made up of a few hundred cells to be alive will protest that embryo's destruction.

This is a legitimate argument based on when someone believes life begins. But some protests I heard were from people worried about embryonic stem cells being used to clone humans. What I can't figure out is why anyone would want to clone someone.

Cloning won't be like it is in the movies. Scientists won't take a cell from someone and make an exact copy of a person who is the same age and has the same memory.

Instead, a human will be cloned like any other mammal. First they'll remove the DNA-containing nucleus from an egg. Then they'll fuse that egg with a cell from the person they want to clone.

This "fertilized egg" will then have to grow and develop in a surrogate mother, be born, and then have to grow up. The clone won't have any of the original's memories.

In essence, a clone would be more like an identical twin who has been reared apart from his or her twin. Even though identical twins reared apart have a lot of similarities, they have a lot of differences, too. One article I saw put the amount of behavior/personality similarity due to genes at something around 50%.

And a clone will probably be more different than that. When the cell's nucleus is put into the egg, scientists erase a lot of the markings on the DNA that originally turned it into an adult cell. This "fertilized egg" is now a blank cell which can be shaped by both its genes AND its environment.

Identical twins develop in the same womb at the same time and so are exposed to the same sorts of environmental effects. A clone would not be. And these environmental factors can affect how we develop. They can even alter DNA and as a result, alter who we become.




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Predicting Fossil Finds

March 2nd, 2009 by Dr. Barry Starr

Scientists used evolutionary theory to figure out where
to find the bones of this fishibian.
Lately I have been reading Jerry Coyne's Why Evolution is True. And so far it is a fascinating read.

What is so great about this book for a scientist is that it gives the big picture on evolution. This sort of thing can be hard to get sometimes because we scientists are so specialized. As I like to tell people, I worked on a single amino acid of a single human protein for my postdoctoral project. For three years.

Coyne's book synthesizes genetics, anatomy, biogeography, physiology, paleontology, geology, and lots of other "ologies" to show how strong the case is for evolution. This is great for me because, of course, I tend to focus on genetics and molecular biology and spend less time on the other fields. Which means I miss important, subtle nuances to some big findings.

For example, I had heard about the fossil of Tiktaalik roseae that was found in 2004 that linked fish to amphibians. This was a huge deal because the animal that the bones came from had characteristics of both fish and amphibians. And it appeared in the fossil record at the right time to be a transitional animal between the two.

What I hadn't fully appreciated was that the scientists decided to look where they did based on how old they thought the fossil should be. In other words, they were able to use the theory of evolution to predict where to find the fossil they were looking for.

They knew from previous fossil finds that something like Tiktaalik roseae would have appeared between 360 and 390 million years ago. The scientists also knew from previous research that the beast would have been in freshwater. So they got out a geological map and looked for places that met these criteria. They settled on Ellesmere Island in Canada and after five years, they found this marvelous fossil.

This is important for a lot of reasons. One is that it obviously tells us a lot about how vertebrates emerged onto dry land. Another is that it provides further validation of geological dating methods. They had to rely on these methods to know where to look for the fossil and the methods worked.

This find is also important because it is based on a prediction made by evolutionary theory. Around 390 million years ago, the only vertebrates were fish. By 360 million years ago, there were four-footed vertebrates on land. So the scientists looked in a place that was 375 million years old.

Scientists used evolution to make a testable prediction that turned out to be true. And evolution came through with flying colors like any good scientific theory should.




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Posted in Biology, Partners | 2 Comments

Happy Birthday Charlie!

February 17th, 2009 by Dr. Barry Starr



This month marks the 200th birthday of Charles Darwin and the 150th anniversary of On the Origin of Species. If Darwin were alive today, I think he would be very pleased.

He would undoubtedly be very excited about everything we've learned about biology since his time. Like the rest of us, he would be awed by the beauty, grandeur, and complexity of life on Earth.

He would also be pleased that his ideas about natural selection and evolution are to date the only scientific explanation for all of this. His ideas pervade every aspect of modern biology from medicine to genomics to ecology.

His theories dominate because they are supported by mountains of evidence (Read Why Evolution is True to find out more about the data that supports evolution. You can click here for a review of the book.). The evidence in support of evolution is so overwhelming that there is no real debate about it among biologists.

Of course, like any scientific theory, not every "t" is crossed nor every "i" dotted. But that is more of a reflection on how science works rather than the theory itself.

A scientist gathers some data and then proposes a hypothesis to explain that data. Then the scientist does some experiments to test the hypothesis. The new data either supports the hypothesis, requires that the scientist modify the hypothesis to fit the new data, or requires the scientist to come up with a new hypothesis that better explains the data. Then scientists repeat this process over and over again until the hypotheses can be unified into a theory.

This has gone on for 150 years or so for evolution and if anything, evolution is stronger than it was before. Sure, every now and then a hypothesis within the theory needs to be modified but the theory remains as strong as ever.

In fact, no point of contention has yet been raised that is the straw that will break evolution's back. And there is nothing obvious on the horizon that will.

Darwin would also probably not be surprised that his theory remains controversial because it seems to fly in the face of a Creator. Which is of course nonsense. Despite worries about how Earth being the center of the Universe would cast doubts on the Creator, Christianity survived Copernicus and Galileo. And it will survive Darwin as well.

I heard this interesting interview on NPR over the weekend with Richard Dawkins about his book, The God Delusion. In the interview, Dawkins states that it seems unlikely to him that God would create a Universe that could be explained by natural causes. I disagree.

My understanding is that Christianity is based on faith. If a Creator made the Universe in such a way that scientists could show the Earth was 10,000 years old, then of course a Creator exists. That is the only possibility. So where is the faith in that? How would it be different than the Creator greeting each person and welcoming him or her to the Creator's Universe?

To me it makes sense that a Creator would make a world that was or could be formed naturally. In which case it doesn't really matter scientifically whether life arose on Earth through a Creator or by chance. Both ways require evolution. Thank you Charles Darwin for giving us this great framework within which we can understand life here on Earth.




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Posted in Biology, KQED, Partners | 7 Comments

A Long and Winding DNA

February 2nd, 2009 by Dr. Barry Starr

There is an awful lot of DNA stuffed into every cell.Ben's blog on stars and grains of sand got me to thinking about DNA. How long would the DNA from every living thing on Earth stretch? Could we make it to the next star? The next galaxy? The end of the Universe?

Let's start out with people. Each human cell has around 6 feet of DNA. Let's say each human has around 10 trillion cells (this is actually a low ball estimate). This would mean that each person has around 60 trillion feet or around 10 billion miles of DNA inside of them.

The Earth is about 93 million miles away from the sun. So your DNA could stretch to the sun and back 61 times. That is one person’s DNA.

The best estimate I could find of the world’s population of people is around 6.7 billion. When we multiply 10 billion miles of DNA by 6.7 billion, we end up with, well, a really big number. Something like 6.7 X 10¹⁹ or 67 quintillion miles. That is too big a number so let’s convert this to light years.

A light year is around 6 X 10¹² miles. So all human DNA would stretch 11.2 million light years. The closest star to Earth (besides the sun) is around 4.2 light years. So we shoot way past that! The Andromeda galaxy is about 2.5 million light years away from us so human DNA could stretch there and back two or three times.

What if we add the rest of the DNA on the planet? It would obviously be much farther but it is hard to calculate because we don’t know how many plants, animals, bacteria, fungi, etc. there are on the planet. We also don’t have detailed information about every species on Earth.

Let's add bacteria to the mix. I decided on this because we know how many cells are in a bacterium—one.

One number I saw was that there are 5 X 10³⁰ bacteria on Earth. Bacterial DNA tends to be a lot smaller than human DNA so there will be less of it per cell. Let's say on average there is 4 million base pairs of DNA/bacterium (this number could be off by a very lot). This translates to around .05 inch of DNA per bacterium which means you need to scrape together around 1.3 million bacteria to get a mile of DNA. So all the bacteria in the world have about 3.5 X 10²⁴ miles of DNA.

How far is 3.5 X 10²⁴ miles of DNA? Well, it is about 640 billion light years of DNA. The end of the observable Universe is about 14 billion light years away. So if we stretched out bacterial DNA it would go to the end of the Universe and back around 23 times. Of course it would be incredibly thin and so actually doesn't take up much space in the Universe.

So that's just human and bacterial DNA. (Well, mostly bacterial since human is so piddly in comparison.) I haven't added all of the rest of the DNA out there. I'll leave that to you.




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