QUEST Community Science Blog

Human and chimpanzee chromosomes are very similar.
Note that human chromosome 2 is very similar to a
fusion of two chimpanzee chromosomes.

For the last few weeks I have been corresponding with someone about intelligent design (ID). More specifically, we have been chatting about why humans have 46 chromosomes and most of the great apes have 48.

To me, this is great evidence for evolution. Why? Because if you look at the chromosomes closely, you can see that human chromosome 2 is really just a fusion of two great ape chromosomes.

The idea is that a few million years ago, a common human-chimpanzee ancestor of ours had two of his or her chromosomes fused together. This sort of thing happens all the time even today. Around 1 in 1000 live births has one of these kinds of fusions.

Then, probably through chance,this ancestor with the fused chromosomes went on to found the human race. Now people have 46 chromosomes and chimpanzees have 48.

An alternative explanation is that the designers fused the two chromosomes together when they created humans. The idea would be that the designer wouldn’t create every plant, animal, bacteria, and virus from scratch–why reinvent the wheel every time? Instead the designers would mix and match parts that worked.

So as part of the process of designing a human, the designer fused two ape chromosomes together. This would presumably be simpler than creating a human chromosome 2 the way the other chromosomes were made.

The difficulty with this idea is that there is no obvious advantage to having 46 chromosomes instead of 48. What matters is our DNA, not how it happens to be packaged.

It is possible that there was some advantage to fusing the chromosomes together. For example, maybe a new gene was created at the fusion point. Or maybe genes that were shut off before were now turned on in the new fused chromosomes.

There isn’t any evidence of these kinds of things. And even if there were, a designer who can easily put in the 60 million or so differences between humans and chimpanzees should be able to accomplish whatever results a chromosome fusion gives more elegantly than sticking two ape chromosomes together.

Also, when you look at the fusion point, you can see that the DNA isn’t exactly what you would expect if a fusion happened in the last 10,000 or even 100,000 years. The results look more like an event that happened millions of years ago.

The ends of a chromosome have a defined sequence of DNA repeats called a telomere. The DNA at the fusion point looks very similar to a string of telomeres (as we would expect from a fusion) but it isn’t perfect. This is just what you would expect if the fusion happened millions of years ago. Because our DNA gets changed a little all of the time.

The environment or even our own cells can cause the wrong letter to end up in our DNA. Our cells are pretty good at fixing these mistakes but they don’t catch them all. What this means is that our DNA builds up mutations over time.

When an unfixed change happens in a sperm or egg, then it is passed down to the next generation. If the changes that aren’t fixed happen somewhere important, then they are selected for or against. But if they’re neutral, then they just build up over time. Scientists can even use these sorts of errors to predict how long ago something happened. Or to trace human migration patterns.

These DNA changes at the fusion point do not fit with ID if they don’t serve a purpose. Otherwise, why put them there? It will be interesting to see the results of experiments that might show if these sequences matter or not.

Dr. Barry Starr is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA.

These fish can tell us a lot about ourselves.

Species often end up a different color when their environment changes. And humans are no exception.

When people moved out of Africa tens of thousands of years ago, they were dark-skinned. Now when we look around Northern Europe or parts of Asia, we see much lighter people. What happened?

A common explanation has to do with sunlight and vitamin D. When people moved north, they got less sun. Less sun means less vitamin D and awful diseases like rickets.

Anyone who moved north and had lighter skin ended up getting more vitamin D and did better than their darker neighbors. After awhile, most of the population had light skin.

This is all well and good, but what happened at the gene level to cause this transformation? One way scientists are learning about how humans ended up with lighter skin is by studying fish. For example, the zebrafish has taught us a lot about why Europeans are often so pale.

The zebrafish is an important model system that scientists use to study vertebrate development, human disease, and lots of other things. A common mutant fish that scientists use in these studies is called “golden.” These fish have lighter, yellowish stripes instead of black ones.

Scientists discovered that these mutant fish had yellow stripes because of a single DNA difference (or SNP*) in their SLC24A5 gene. When fish have this DNA difference, they have yellow stripes.

These scientists next looked for this gene in people. What they found was that most of the people they looked at had two copies of the “black stripe” version of the gene. Except for Europeans. They tended to share a common SNP in their SLC24A5 gene that the scientists went on to show is a big part of why many Europeans have lighter skin.

Another group of researchers decided to dig a bit deeper and find out when this transformation happened. By looking at the DNA around SLC24A5, they found that lighter skin came to dominate Europe around 6,000-12,000 years ago. At first this result is a bit confusing because humans moved into Europe around 40,000 years ago. Why did it take so long for lighter skin to become the norm?

Scientists can’t know for sure but one idea is diet. Around this time, Europeans started to grow their own food. And a farmer’s diet has less vitamin D than does a hunter-gatherer’s diet. Maybe the lack of sun only started to affect Europeans after they started growing their own food. Then, after a relatively brief time, most Europeans ended up fair-skinned to get enough vitamin D.

This gene doesn’t explain all of skin color. For example, it doesn’t explain the difference in color between Northern and Southern Europeans. Or why some Asians have fair skin. But it does explain a good deal of European coloration. Thanks, zebrafish!

*SNP=single nucleotide polymorphism

Dr. Barry Starr is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA.

DNA magnified 850,000 times through a scanning electron
microscope
DNA day is coming up on Friday April 25th. This annual celebration of genetics and genomics was set up in 2003 to commemorate the sequencing of the human genome and the 50th anniversary of the solving of the structure of DNA.DNA day was thought of as an opportunity for teachers, students, and the general public to learn about DNA. And to have fun with it.

This should be a chance to pull DNA out of beef, strawberries, kumquats or even yourself and learn that you have around 100 billion miles* of DNA inside of you. In case you’re interested, that’ll reach from the Earth to Pluto and back when Pluto is farthest from Earth. And that is one person’s DNA.

Add up everyone’s DNA in the world and you get 125 million light years of DNA. (At least I think you do… these numbers are getting ridiculous!) That’ll get us to the galaxy Andromeda and back 25 times. Add up all the DNA on Earth and… OK, that’s probably enough of that.

There isn’t just a lot of the stuff but it is amazing to me how similar all human DNA is. The latest estimates are that people are around 99.5% the same at the DNA level. That means that all those light years of DNA are mostly the same old thing just copied over and over.

Notice the mostly. With 6 billion letters of code in every person, a 0.5% difference means 30 million differences between you and me. It is these differences that make me look different than you. And to a varying degree, make me act differently than you.

This code doesn’t work in a vacuum either. The environment can change how it works which is a big reason identical twins aren’t really identical. And one of the reasons why it is so hard to figure out the genetics of complicated diseases like diabetes or heart disease.

Our DNA also changes with time. Things in the environment might damage it. Or our own cells can make mistakes when they make copies of themselves. What this means is that today’s light years of human DNA will be different than the same stretched out DNA in 100 years.

This also means that you have some cells in your body have different DNA than the rest of your cells. And if a DNA change happens in sperm or egg cells, then they are passed on to the next generation. Which is where all the wonderful diversity around us originally came from.

As you can see, there is a lot about DNA to celebrate. It is huge and mysterious and we’re just starting to get a good grasp on what it is all about.

I plan to spend the morning of DNA day at The Tech Museum in San Jose exciting kids (and hopefully some adults) about DNA by running five different hands on genetics programs all at once. It’ll be a blast!

I have searched high and low for a list of DNA day activities here in the bay area but I haven’t come across any. Does anyone know about other DNA day celebrations here in the bay area?

* Each cell has 6 feet of DNA and we are made up of around 50-100 trillion cells.

Dr. Barry Starr is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA.

There is a lot we don’t know about our DNA and how it works. While there seems to be news every week about genetics, scientists are still in the early stages of finding out what effect our genes have on us (check out this post from another QUEST blogger, Dr. Barry Starr). That’s what the researchers at the Canine Behavioral Genetics Project are doing. But in this case, they’re looking at dog DNA.

It turns out that human intervention in the form of hundreds of years of dog breeding has created a unique genetic experiment. Because purebred dogs are in essence closed gene pools, it’s much easier for scientists to compare of DNA of dogs within a breed. The Canine Behavioral Genetics Project is doing this to find the genes that are associated with behavioral disorders, like anxiety and fear. They also hope to use that information to find the genes in humans that are associated with similar disorders.

Millions of problematic dogs are given up each year in the U.S. And while the UCSF team definitely believes that training is a huge part of dealing with dog behavioral disorders, they’re also hoping to understand the genetic influences. Many owners are starting to use medications to help treat these problems, like doggie Prozac. But Melanie Chang, a member of the UCSF team, made a good point to me. Owners tend to think their dog’s problems are the owner’s fault. Sometimes there are other forces at work.

Listen to “Doggie DNA: Human Genetics through Dogs” online, as well as find additional links and resources. Also, check out the photo set with behind-the-scenes photos.

Lauren Sommer is an Associate Media Producer for QUEST.

Last night, I watched a reality dating show with a seemingly wacky way of finding true love. The male searching for love sniffed the armpits of potential females. He either turned away in disgust or became quite aroused by the wafts of underarm aroma. What is so comical is that a new dating service relies on a more sterile but ultimately similar approach. Scientific Match, which opened last December, provides dating services based on both personality and DNA compatibility. Clients send in a cheek swab of DNA to be matched up with a potential mate who has dissimilar DNA.

Attraction based on dissimilar DNA was first studied in 1995 by Claus Wedekind. The study is referred to as the “Sweaty T-Shirt Experiment.” In the study, women were given t-shirts recently worn by men. The men in the study were not allowed to wear any cologne or scent that would mask their natural scent. The women were then asked to rate how “sexy” the t-shirts smelled to them. Correlation was found between how good the shirts smelled to the women and how dissimilar their immune DNA was to the man in question. Following this approach, Scientific Match matches clients based on chemistry, specifically making sure six immune genes of each male and female do not match.

But why would it be advantageous to be attracted to someone with dissimilar DNA? Scientifically speaking, it increases the robustness of the species by providing genetic diversity in a gene pool. Diversity enables survival in intense bouts of environmental and infectious selection. There is more of a chance that an individual will have the adaptation to survive and propagate in the population and pass on the advantageous trait. Similar DNA creates a bottleneck in the gene pool because similar genes are passed down rather than diversified - this is the case with inbreeding.

However, basing attraction on chemistry has its drawbacks. Women who are on birth control are turned away from Scientific Match because findings have reported that they are attracted to men with similar immune system genes. Birth controls works by tricking the body in believing it is pregnant. Studies have shown this also changes the indication of genes making women more attracted to family members than potential mates. This behavior has been seen in other mammals and is thought to be a way of protecting a pregnant member of the family and its offspring from harm.

If you meet the qualifications for Scientific Match, you might just find the love of your life for a whopping price tag of a $1,995. That or you can try the more wacky approach of smelling someone’s armpits! Either way, companies such as these denote advances in technology. DNA sequencing and comparative genomics have become cutting edge science and they are infiltrating our everyday life. Genetic testing is not only in the dating arena. Swab and send testing kits are being used for other projects such as National Geographic’s Genographic Project and 23andMe. Both use DNA to uncover deep roots of family trees by using comparative DNA.

Cat Aboudara is the Special Projects Manager at California Academy of Sciences and works in the public programs division. The Academy is a wonderful fit for her because of her curiosity about the natural world and her experience in working with native California wildlife.

We are all Africans in our DNA.

We all originally came from Africa. At least that is what a couple of new studies have claimed.

Now this isn’t breaking news. Other studies have looked at people’s DNA and proposed the “Out of Africa” hypothesis. What is different with these studies is how many people they looked at. And how much of their DNA.

One study looked at over 500,000 DNA differences in 438 people from 29 different populations. The other looked at over 600,000 differences in 938 people from 51 different populations. This dwarfs any other previous study.

All of this data showed that East Africans had the most diverse DNA. And that the further away a population got from East Africa, the less diverse their DNA was. So how does this show that we are all Africans at heart (or at least in our DNA)?

It has to do with the fact that DNA changes over time. Everyone’s DNA is a little different from when they were a fertilized egg because of DNA mutations.

If a change happens in the DNA of an egg or sperm cell, then it will be passed to the next generation. So the group that stays longer in one place will build up more of these changes. Their DNA will be more genetically diverse.

Imagine it is 50,000 years ago and our ancestors are all in Africa. These folks have been there for hundreds of thousands or even millions of years. Over this time, there were lots of individuals all mixing their DNA. And their DNA was changing slightly generation to generation.

Now imagine that a few people develop a bit of wanderlust. They’re tired of Africa and want to see what the Arabian Peninsula looks like. So a small group takes off and heads over there. And doesn’t return.

This group, which will go on to found Asia’s population, is not nearly so diverse as the group they left behind. And the smaller the founding group, the less diverse their DNA will be.

Now 50,000 years later, here we are. East Africans have continued to mix and change from their big diverse starting population. Asians have mixed and changed too but from a smaller, less diverse starting population. So the East Africans are more genetically diverse than the Asians.

Now imagine it is 10,000 years ago. A small group of Asians heads over to Alaska and doesn’t return. This starting group is even less diverse than the original group of East Africans. Which helps explain why Native Americans are genetically less diverse than Asians.

The studies were so big that they were able to make even finer distinctions (see the tree to the right). And as data continues to pour in (especially from companies like 23andMe and DeCODEme),
scientists will be able to refine ancestry even further.

Dr. Barry Starr is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA.

latitude: 0.213671, longitude: 16.9849

Companies like GenoCAD allow users to piece together
their own designer DNA.

“Synthetic biology” seems like a contradiction in terms, doesn’t it? I mean, if it’s biological, it’s natural, right? And if it’s natural, then it’s not synthetic.

Sure. Except that modern science has sorta blurred all those nice convenient boundaries.

Nothing has demonstrated this more clearly than Craig Venter’s latest feat of building out an entire bacterial genome from scratch. It’s the second episode of a three-part plan, devised by the venerable entrepreneur who brought the world its first look at the human genome, to create an organism with a manmade DNA sequence. First, he took a genome from one bacterium, stuck it into an empty cell, and then got it going. Now he’s pieced together a copy of the DNA of Mycoplasma genitalium, the second-smallest known bacterial genome. The last in this troika of tricks will be to combine these two steps, inserting the manufactured genome into a cell and starting it up.

Some scientists believe that success in this endeavor will soon lead to the creation of organisms with new, artificial genomes. Couple that idea with the announcement that researchers at Scripps have devised two new molecules that can function as DNA bases and the question of what’s alive, even what counts as biology, gets a little fuzzy.

I first heard about synthetic biology several years ago, at a lecture for science writers. The speaker had culled together sections of DNA that he hoped would produce a medically useful enzyme, inserted the sequences into a bacterial genome, then let the bug do its work copying the gene and producing the chemical, which the speaker could then harvest.

This seemed to me to be a fundamentally different way of thinking about biology. Here was a scientist who wasn’t asking: “How does this work?” or “Isn’t the living world amazing?” He was asking: “How can I employ this system to manufacture a specific product for my benefit?” He was harnessing the ingenious mechanisms of biology as tools. Being able to put together sequences of DNA seemed akin to the invention of movable type, a letter here, a letter there, till you spell the words (or in this case, genes) you want.

At some level, I was offended by this, though I’m still not exactly sure why. It seemed like a disrespectful exploitation of life. Who are we to manipulate the code defining living things and make them do our bidding? And how far will we go with this? Will the precious genomes of my plants, or my pets, or even me for Godsakes be manipulated one day, ordered to pump out some substance that a distant researcher has deemed desirable?

On the other hand, I was fascinated. The potential this technique held for research was enough to send a geek’s mind reeling. What amazing ingenuity. What creative thinking. How wholly human, actually, to devise a new purpose for knowledge we’d gained. This engineering feat struck me as demonstrating a deep appreciation—almost a reverence for—the power within the systems that the living world has evolved.

So there I was, conflicted.

Since then, this process of connecting DNA bits together has become more commonplace. So common, in fact, that a variety of companies, like Gene Design and GenoCad invite you design a gene online and have it sent to you (Go ahead, try it. It’s easy to make up valid sequences.). This is, in fact, what Venter did: ordered sequences of DNA and pieced them together, discovering that he could make an exact copy of the genome he desired.

Synthetic biology’s proponents promise microbes that can clean up pollution, produce drugs, signal changes in the environment, help with medical diagnoses, and a slew of other useful tasks. Its detractors fear the creation of new biological weapons, and new organisms that aren’t well understood but which may be able to reproduce and evolve.

Since this sort of talk makes a sci-fi world of ready-made critters seem like it’s just around the corner, it’s easy to forget how much work remains before our best (or worst) dreams come true. Just because we can string functional bits of DNA together, even whole (though relatively small) genomes, doesn’t mean that we actually know much about how they work. Venter, after all, didn’t invent a new genome, he just put an already-known one together. The goal, of course, is to be able to someday make new genes that do specific things. But for the moment, synthetic biologists hope to use the technologies they’re developing to learn much more about how genes work in the first place.

What does wait for us around the corner is a set of questions similar to those that accompany all new and emerging technologies. How do we create policy to protect ourselves from the risk but not quash research? Who decides what research directions and questions are most important to pursue? How do we create profit incentives for technology that benefits the common good?

And will I ever resolve my mixed feelings about this new science? Is it better off that I don’t?

Robin Marks is a journalist and science writer who current serves as a Multimedia Projects Developer for the Exploratorium in San Francisco, CA.

latitude: 39.1067, longitude: -77.1623

ABC, Yahoo! and others ran a story about a woman who had a liver transplant whose blood type ended up changing. I love stories like this.

Not because of the change itself. Most likely, stem cells traveled from the new liver to the patient’s bone marrow. There, the stem cells set up shop and gave her a new blood type.

What intrigues me is what these types of stories mean for solving crimes. Because changed blood type usually means changed blood DNA. In other words, her blood cells now have different DNA from the other cells in her body. This can really confound an investigation if the police aren’t careful.

Of course this was a very rare event. But bone marrow transplants aren’t. And every bone marrow transplant results in blood cells with different DNA compared to the rest of the recipient’s cells.

Imagine that someone who has had a bone marrow transplant does something wrong and leaves blood behind at the crime scene. The police do a cheek swab to gather DNA evidence and check it against the police DNA database as well as likely suspects (including our bone marrow recipient).

The police don’t catch our bone marrow recipient because his cheek DNA is different than his new blood DNA. So he is off the hook (as long as the police don’t check the blood too). But they do get a match and arrest someone—the donor.

Sounds weird but something almost like this complicated a case in Alaska a few years ago. There was a serious crime and a semen sample from the crime scene matched a known criminal’s DNA. But the person whose DNA matched the DNA from the crime scene had a strong alibi…he was in jail at the time! So what happened?

A little further investigation showed that the guy in jail had received a bone marrow transplant from his brother. And his brother was the one who committed the crime.

This one worked out all right in the end. But what would have happened to the brother if he weren’t in jail at the time? Would an overworked public defender have figured something like this out? The guy was lucky he was already in jail!

So people with bone marrow transplants need to be careful. And the police need to be careful about what sample they take from suspects.

Dr. Barry Starr is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA.

latitude: -33.8027, longitude: 150.988