Darwin’s Pigeons Meet The Genomic Age Like many naturalists of well-heeled social standing in his era, Charles Darwin was fond of keeping pigeons. While we now view these ashy sky-rats as something of an urban blight, there was then (and still is) an enormous group of breeding hobbyists worldwide. Bred for characteristics like frilled hoods and feathery spats (they really do look ridiculous), it’s these captive breeds that are believed to have escaped and become the feral urban populations of today. Even before Darwin’s famous finches of Galapagos, he viewed pigeon breeding as Nature’s power of genetic selection put in the hands of man. All of this decades before the idea of a gene, much less the DNA that a gene is made of, was born in the minds of scientists. More than a century and a half later, a team led by Utah’s Michael Shapiro has sequenced the genomes of 40 of these couture birds, to try and connect the age of Darwin with the age of the genome. It appears that all the world’s pigeons descend from one species, the rock pigeon of the Middle East. They flocked to man’s earliest farms in Mesopotamia, and were quickly domesticated for use as food, messengers and pets, a tradition which continues today. By digging down into the DNA base differences between various breeds, they hope to draw a map of pigeon evolution that would not only prove Darwin most definitely correct, but also make him quite happy. Carl Zimmer has the whole, wonderful pigeon tale at The New York Times. Oh, and one last tidbit: That frilly hood up there? It’s caused by a gene called EphB2 being turned on in a place it’s not supposed to be. The more you know … (pigeon photos via NY Times, by Richard Bailey)
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Darwin’s Pigeons Meet The Genomic Age Like many naturalists of well-heeled social standing in his era, Charles Darwin was fond of keeping pigeons. While we now view these ashy sky-rats as something of an urban blight, there was then (and still is) an enormous group of breeding hobbyists worldwide. Bred for characteristics like frilled hoods and feathery spats (they really do look ridiculous), it’s these captive breeds that are believed to have escaped and become the feral urban populations of today. Even before Darwin’s famous finches of Galapagos, he viewed pigeon breeding as Nature’s power of genetic selection put in the hands of man. All of this decades before the idea of a gene, much less the DNA that a gene is made of, was born in the minds of scientists. More than a century and a half later, a team led by Utah’s Michael Shapiro has sequenced the genomes of 40 of these couture birds, to try and connect the age of Darwin with the age of the genome. It appears that all the world’s pigeons descend from one species, the rock pigeon of the Middle East. They flocked to man’s earliest farms in Mesopotamia, and were quickly domesticated for use as food, messengers and pets, a tradition which continues today. By digging down into the DNA base differences between various breeds, they hope to draw a map of pigeon evolution that would not only prove Darwin most definitely correct, but also make him quite happy. Carl Zimmer has the whole, wonderful pigeon tale at The New York Times. Oh, and one last tidbit: That frilly hood up there? It’s caused by a gene called EphB2 being turned on in a place it’s not supposed to be. The more you know … (pigeon photos via NY Times, by Richard Bailey)
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Darwin’s Pigeons Meet The Genomic Age

Like many naturalists of well-heeled social standing in his era, Charles Darwin was fond of keeping pigeons. While we now view these ashy sky-rats as something of an urban blight, there was then (and still is) an enormous group of breeding hobbyists worldwide. Bred for characteristics like frilled hoods and feathery spats (they really do look ridiculous), it’s these captive breeds that are believed to have escaped and become the feral urban populations of today.

Even before Darwin’s famous finches of Galapagos, he viewed pigeon breeding as Nature’s power of genetic selection put in the hands of man. All of this decades before the idea of a gene, much less the DNA that a gene is made of, was born in the minds of scientists.

More than a century and a half later, a team led by Utah’s Michael Shapiro has sequenced the genomes of 40 of these couture birds, to try and connect the age of Darwin with the age of the genome. It appears that all the world’s pigeons descend from one species, the rock pigeon of the Middle East. They flocked to man’s earliest farms in Mesopotamia, and were quickly domesticated for use as food, messengers and pets, a tradition which continues today. By digging down into the DNA base differences between various breeds, they hope to draw a map of pigeon evolution that would not only prove Darwin most definitely correct, but also make him quite happy.

Carl Zimmer has the whole, wonderful pigeon tale at The New York Times. Oh, and one last tidbit: That frilly hood up there? It’s caused by a gene called EphB2 being turned on in a place it’s not supposed to be. The more you know …

(pigeon photos via NY Times, by Richard Bailey)

DNA: The Book of You

Oh hey, some guy with the same name as me and who sounds exactly like me wrote and narrated this video for TED-Ed all about the scale, structure and organization of the human genome.

Oh wait… it IS me! Enjoy the sciencey sounds of my voice telling you all about how big the human genome is.

Although 20,000 genes sounds like a lot, it’s far less than the number scientists initially predicted. We end up getting lots of variants out of fewer genes thanks to something called alternative splicing. Although none of it is “junk”, about 8% of our genome is inactive virus DNA (which we stole genes from in order to be born), and more than half is other kinds of insertions from ancient, jumping “selfish genes” called retrotransposons.

Enjoy!

(A note: Most of the numbers in this lesson are for one copy of the human genome. Remember that you actually have two copies of the human genome in every cell, so the length of DNA and number of bases, etc. it actually DOUBLE that! If you want to know more details about any of the facts and figures in the video, leave me a note in the YouTube comments or send me a message here or on Twitter.)

Source: youtube.com

The Story of You: ENCODE and the Human Genome

Encompassing the largest analysis of human DNA sequences since the Human Genome Project, the ENCODE project has provided scientists with the most comprehensive look yet at what is going on in the “rest” of our genome. It’s a very cool thing, and a Big Deal™. Of course, it’s not the first time that we’ve been told that important things are happening elsewhere in our genome, and it probably has quite a few chucks of data in it that won’t pan out. But hey, that’s science.

Even if the research teams (dozens of them!) raised a few eyebrows with the way they announced the data, ENCODE is still a major milestone in deciphering the function of the darker regions of the human genome. Here’s a video to introduce what it means.

I’ll have more on what the ENCODE project found later this week! Should be a fun exploration.

(video by NatureVideoChannel)

Source: youtube.com

There’s Always Genes IN the Banana Diagram Why a banana genome Venn diagram is so important I know it can be pretty confusing to post random images from research manuscripts without any context to why they’re interesting or significant, but this is a pretty genius way of delivering a bunch of banana data all at once (see what I did there?). As more and more genomes are fully sequenced, there’s a lot of focus being put on how many genes and other DNA clusters are shared between distantly (or closely) related organisms. This figure represents how many genes the wild banana (Musa acuminata) shares with five of its monocot cousins. We’ve talked a bit about Venn diagrams before, and up until now I had only seen five categories represented on one chart. But with the addition of this banana, that record stands at six. The banana genome was recently sequenced (you can see the paper here if you have a subscription to Nature, which no one outside of a college campus does), with hopes that understanding its makeup can help toughen up the delicate, weakened commercial crop we eat by the truckload. You see, since their domestication 7,000 years ago, wild bananas have been extensively selected, crossed and inbred to create the soft, sweet yellow banana that we see in stores today. But as a result of this selective breeding, modern bananas have almost no genetic diversity, making them extremely vulnerable to pests and disease. Viruses and infection are actually threatening to eradicate banana crops worldwide within 20 years, which would be a very disappointing blow to my breakfast table. By understanding how the wild banana’s genes are organized and how they function, perhaps we can engineer or breed a fruit to last. For more, check out this in-depth story in the Los Angeles Times. (↬ Boing Boing)
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There’s Always Genes IN the Banana Diagram

Why a banana genome Venn diagram is so important

I know it can be pretty confusing to post random images from research manuscripts without any context to why they’re interesting or significant, but this is a pretty genius way of delivering a bunch of banana data all at once (see what I did there?).

As more and more genomes are fully sequenced, there’s a lot of focus being put on how many genes and other DNA clusters are shared between distantly (or closely) related organisms. This figure represents how many genes the wild banana (Musa acuminata) shares with five of its monocot cousins.

We’ve talked a bit about Venn diagrams before, and up until now I had only seen five categories represented on one chart. But with the addition of this banana, that record stands at six. The banana genome was recently sequenced (you can see the paper here if you have a subscription to Nature, which no one outside of a college campus does), with hopes that understanding its makeup can help toughen up the delicate, weakened commercial crop we eat by the truckload.

You see, since their domestication 7,000 years ago, wild bananas have been extensively selected, crossed and inbred to create the soft, sweet yellow banana that we see in stores today. But as a result of this selective breeding, modern bananas have almost no genetic diversity, making them extremely vulnerable to pests and disease. Viruses and infection are actually threatening to eradicate banana crops worldwide within 20 years, which would be a very disappointing blow to my breakfast table.

By understanding how the wild banana’s genes are organized and how they function, perhaps we can engineer or breed a fruit to last.

For more, check out this in-depth story in the Los Angeles Times.

(↬ Boing Boing)

Source: Boing Boing

DNA from Cavemen Bones Unlock Pieces of Oldest Human Genome to Date About 7,000 years ago, high in Spain’s northern Cantabrian mountains, a pair of weary hunters took refuge in a deep cavern, never to emerge again. Until 2006, that is, when these early humans were uncovered by cave explorers. Dating from pre-agricultural Europe, these remains predate Ötzi the Iceman by nearly two millenia. Recently, scientists were able to piece together about 1% of each caveman’s genome, using techniques right out of CSI: Iceman.  The DNA of these early Iberians does not appear related to modern Spanish and Portuguese, but rather more closely related to Northern Europeans. Certain parts of their DNA show that early Europeans from Poland and Lithuania were brethren of those as far away as Spain … truly nomadic hunter-gatherers! These represent the earliest genome sequences of modern humans. The percentage of the genome that they sequence should go up as the team continues its work, and we’ll know even more about how the earliest humans in Europe contributed to the world we see today. (↬ LiveScience)
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DNA from Cavemen Bones Unlock Pieces of Oldest Human Genome to Date

About 7,000 years ago, high in Spain’s northern Cantabrian mountains, a pair of weary hunters took refuge in a deep cavern, never to emerge again. Until 2006, that is, when these early humans were uncovered by cave explorers.

Dating from pre-agricultural Europe, these remains predate Ötzi the Iceman by nearly two millenia. Recently, scientists were able to piece together about 1% of each caveman’s genome, using techniques right out of CSI: Iceman. 

The DNA of these early Iberians does not appear related to modern Spanish and Portuguese, but rather more closely related to Northern Europeans. Certain parts of their DNA show that early Europeans from Poland and Lithuania were brethren of those as far away as Spain … truly nomadic hunter-gatherers!

These represent the earliest genome sequences of modern humans. The percentage of the genome that they sequence should go up as the team continues its work, and we’ll know even more about how the earliest humans in Europe contributed to the world we see today.

(↬ LiveScience)

Source: livescience.com

Chimps, Bonobos and Us Closest living relative of Homo sapiens? Easy. Chimpanzees, right? It might not be that simple. With the recent sequencing of the bonobo genome, the distinction between the two species is getting fuzzier, as is the question of who’s a closer relative of humans. Bonobos are a small population of chimpanzee-like apes that live in a tiny pocket of the Congo. They themselves split off of the lineage of chimpanzees less than two million years ago after their population was cut off by the Congo river. Unlike the rather aggressive chimpanzees, who are far more widespread across Africa, bonobos are … well, rather less so. Bonobos look so much like chimps (the bonobo is on the right up above) that their behavior is one of the few ways to tell them apart. They are known to settle disputes through sex, the gender combination not always important, with the activity even completed while eating. Sex is their cultural currency. Don’t believe me? Watch this. Chimps do no such thing, to their own recreational detriment. The sequenced bonobo genome only differs from the chimpanzee genome by 0.4% at the DNA level. That’s within the normal variability of chimp genomes! So are they bonobos or are they chimps? How much of species separation is genetic and how much is behavioral? What, if anything in the small genetic difference leads to those huge behavioral changes? And if they are both so closely related, who is our actual closest relative? This is a debate that will continue. (via Ars Technica)
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Chimps, Bonobos and Us Closest living relative of Homo sapiens? Easy. Chimpanzees, right? It might not be that simple. With the recent sequencing of the bonobo genome, the distinction between the two species is getting fuzzier, as is the question of who’s a closer relative of humans. Bonobos are a small population of chimpanzee-like apes that live in a tiny pocket of the Congo. They themselves split off of the lineage of chimpanzees less than two million years ago after their population was cut off by the Congo river. Unlike the rather aggressive chimpanzees, who are far more widespread across Africa, bonobos are … well, rather less so. Bonobos look so much like chimps (the bonobo is on the right up above) that their behavior is one of the few ways to tell them apart. They are known to settle disputes through sex, the gender combination not always important, with the activity even completed while eating. Sex is their cultural currency. Don’t believe me? Watch this. Chimps do no such thing, to their own recreational detriment. The sequenced bonobo genome only differs from the chimpanzee genome by 0.4% at the DNA level. That’s within the normal variability of chimp genomes! So are they bonobos or are they chimps? How much of species separation is genetic and how much is behavioral? What, if anything in the small genetic difference leads to those huge behavioral changes? And if they are both so closely related, who is our actual closest relative? This is a debate that will continue. (via Ars Technica)
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Chimps, Bonobos and Us

Closest living relative of Homo sapiens? Easy. Chimpanzees, right? It might not be that simple. With the recent sequencing of the bonobo genome, the distinction between the two species is getting fuzzier, as is the question of who’s a closer relative of humans.

Bonobos are a small population of chimpanzee-like apes that live in a tiny pocket of the Congo. They themselves split off of the lineage of chimpanzees less than two million years ago after their population was cut off by the Congo river. Unlike the rather aggressive chimpanzees, who are far more widespread across Africa, bonobos are … well, rather less so.

Bonobos look so much like chimps (the bonobo is on the right up above) that their behavior is one of the few ways to tell them apart. They are known to settle disputes through sex, the gender combination not always important, with the activity even completed while eating. Sex is their cultural currency. Don’t believe me? Watch this.

Chimps do no such thing, to their own recreational detriment.

The sequenced bonobo genome only differs from the chimpanzee genome by 0.4% at the DNA level. That’s within the normal variability of chimp genomes! So are they bonobos or are they chimps? How much of species separation is genetic and how much is behavioral? What, if anything in the small genetic difference leads to those huge behavioral changes? And if they are both so closely related, who is our actual closest relative? This is a debate that will continue.

(via Ars Technica)

Continuing “Joe’s Answer Bag Week”: This may be a bold request, but could you post about the percentages of DNA we share with other things? Or a link to something of that nature… From: chiefsfan71308 Hi there, Chief Sfan (is that Nordic?). I know what you’re getting at with this question. The problem is that you aren’t asking the right one, so I am going to answer it differently. I’ll tell you right away that there’s no master list of How Similar The Human Genome Is To X. The percentage of DNA that we share with another organism isn’t as important as what that DNA is doing. Because DNA by itself does not an organism make. It’s actually pretty boring stuff just sitting in a nucleus. Of course, if it didn’t do anything, there’d be no nucleus, no cell, no proteins, no organism. It’s the genes that really matter, and more than that? The proteins that they make. Of the ~3 billion base pairs of DNA in the human genome, only about 1.5% of it codes for proteins (~25,000 genes total, maybe less). The rest? It’s not junk, but it doesn’t produce much of the machinery of life (although it’s really interesting!). A chimpanzee’s genome is about the same size and has just about as many genes. So let’s compare the two, just looking at the genes. If we took the strings of DNA sequence from our genes and compared it letter for letter with a chimpanzee’s gene sequences, we would find that we share >98.5% of our DNA. What’s more, the proteins made from those genes are 99% identical in the amino acid sequence (because some DNA differences could actually be silent in proteins) meaning that our cells produce almost exactly the same machinery of life. Six percent of human and chimpanzee genes are only present in one species or the other, though. That’s probably a big source of why we’re different (for instance, we have far fewer olfactory genes, so we can’t smell for crap). SInce chimps and humans diverged from a common ancestor, out genomes have separated by about 1%. Why is all of this important? Well, humans differ from one another by about 0.1% of their gene sequence. We’re pretty diverse in the way we look and function. Chimps and humans differ from each other by about 15 times that. I can believe it. Can you? Let’s get weirder. About 30% of our genes are totally identical. But some, like a protein called FOXP2, differ in a very particular sequence. What’s special about FOXP2? It’s involved in speech. How different we are is not as important as where we are different. And don’t even get me started on copy number and gene regulation differences! You can extend this same kind of logic down to mice, dogs, yeast, and even bacteria. It’s all part of a field called comparative genomics, and it’s very, very cool stuff. A final note: Whenever I write about our genome and how it has evolved, I find it harder and harder to understand why this sort of direct genetic connection scares evolution deniers and creationists so much. There’s great elegance and beauty in how complex our machinery of life has become as species have diverged through time. And there’s a wondrous sense of connection in nature knowing that what makes me alive is not so different from what makes a yeast alive. The small differences that make us human make me feel that much more special, certainly not less so. For more: Check out the chimpanzee genome project.
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Continuing “Joe’s Answer Bag Week”:

This may be a bold request, but could you post about the percentages of DNA we share with other things? Or a link to something of that nature…

From: chiefsfan71308

Hi there, Chief Sfan (is that Nordic?). I know what you’re getting at with this question. The problem is that you aren’t asking the right one, so I am going to answer it differently. I’ll tell you right away that there’s no master list of How Similar The Human Genome Is To X.

The percentage of DNA that we share with another organism isn’t as important as what that DNA is doing. Because DNA by itself does not an organism make. It’s actually pretty boring stuff just sitting in a nucleus. Of course, if it didn’t do anything, there’d be no nucleus, no cell, no proteins, no organism. It’s the genes that really matter, and more than that? The proteins that they make.

Of the ~3 billion base pairs of DNA in the human genome, only about 1.5% of it codes for proteins (~25,000 genes total, maybe less). The rest? It’s not junk, but it doesn’t produce much of the machinery of life (although it’s really interesting!). A chimpanzee’s genome is about the same size and has just about as many genes. So let’s compare the two, just looking at the genes.

If we took the strings of DNA sequence from our genes and compared it letter for letter with a chimpanzee’s gene sequences, we would find that we share >98.5% of our DNA. What’s more, the proteins made from those genes are 99% identical in the amino acid sequence (because some DNA differences could actually be silent in proteins) meaning that our cells produce almost exactly the same machinery of life. Six percent of human and chimpanzee genes are only present in one species or the other, though. That’s probably a big source of why we’re different (for instance, we have far fewer olfactory genes, so we can’t smell for crap).

SInce chimps and humans diverged from a common ancestor, out genomes have separated by about 1%. Why is all of this important? Well, humans differ from one another by about 0.1% of their gene sequence. We’re pretty diverse in the way we look and function. Chimps and humans differ from each other by about 15 times that. I can believe it. Can you?

Let’s get weirder. About 30% of our genes are totally identical. But some, like a protein called FOXP2, differ in a very particular sequence. What’s special about FOXP2? It’s involved in speech. How different we are is not as important as where we are different. And don’t even get me started on copy number and gene regulation differences!

You can extend this same kind of logic down to mice, dogs, yeast, and even bacteria. It’s all part of a field called comparative genomics, and it’s very, very cool stuff.

A final note: Whenever I write about our genome and how it has evolved, I find it harder and harder to understand why this sort of direct genetic connection scares evolution deniers and creationists so much. There’s great elegance and beauty in how complex our machinery of life has become as species have diverged through time. And there’s a wondrous sense of connection in nature knowing that what makes me alive is not so different from what makes a yeast alive. The small differences that make us human make me feel that much more special, certainly not less so.

For more: Check out the chimpanzee genome project.

I’m still a little bit confused about what this new Nanopore DNA sequencing is…What does it mean to sequence a genome? From: breakfreefromyourstandstill Part of “Joe’s Answer Bag Week” A-la kazaam! Watch me attempt to explain something very complicated using nothing but words … Genomic sequencing is a super hot topic in biology these days, based on how cheap and easy it is becoming (relatively, anyway). It’s easy to forget that some people might not fully understand what that means. This will start out ridiculously basic, but let’s see if I can summarize this in just a few paragraphs: Can you reconcile what a genome at least represents? It’s the nucleic acid information inside every cell (doesn’t matter if it’s a bacterium, a fungus or a human … or a virus) that encodes all the instructions for life (argue amongst yourselves whether viruses are alive). In humans, it is ~3.2 billion base pairs of DNA inside of a nucleus. Everything that a cell can and ever will/won’t do is written in the patterns of this 3.2 billion character string. If we want to know what something in the cell does, like an enzyme or a signaling protein, then we have to know what that enzyme or signaling protein is made of. If we look all the way back in the genome and read the order of DNA bases, it’s like reading an Ikea instruction manual and figuring out what crappy table it makes in the end without actually pulling out those little hex wrenches. It doesn’t always work perfectly that way, but you get the idea. So genome sequencing is just reading the DNA sequence of all the base-pairs in a cell’s instruction manual. But we don’t read them from one end to another, because that’s impossible. Instead we read them in small pieces, and then use powerful computers to put the small pieces together. How we make the small pieces that we read is where it gets really interesting. When the human genome was first sequenced, they basically randomly chopped it up using a tiny amount of starting material. Then they amplified it (made more of each piece) so that they could read it using less sensitive technology and stitch it back together on an Intel 486 running Windows 98. It was sort of like reading a sentence three times to make sure you get it exactly right. But when you amplify DNA, you introduce errors and you end up with something like a book with a typo on every page (or sometimes missing whole pages altogether). It was also super F-ing expensive to do it, and it took ten years. Since then, biology has been trying to make the process of reading DNA sequences cheaper, faster, and requiring less starting material. Nanopore sequencing is the newest and most bang-pow hotshot method that anyone’s invented.  Imagine you are sitting on a sheet full of holes. The holes are just barely big enough to fit a strand of DNA through. Up through the middle you start pulling a single, tiny DNA strand, like thread through a needle’s eye. Thanks to your expert vision and extremely advanced biology knowledge, you can recognize each of the four DNA bases as you pull the string through, one-by-one. You copy them down on a piece of paper next to you, and pretty soon you’ve read an entire string of DNA, much longer than you could have with old technologies. That’s nanopore sequencing. It’s pulling a single strand of DNA through a tiny hole that reads every base as it passes by. If you have thousands and thousands of those tiny holes, you can put together an entire genome from a bunch of single molecules, using powerful computers. It’s fast, cheap and it (hopefully) doesn’t have the gaps and typos that old-school sequencing does. Sequencing an entire genome could now take as little as a day, and for less than a few thousand dollars. FOR MORE: Check out this post and this post to see some cool videos and stats about nanopore sequencing.
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I’m still a little bit confused about what this new Nanopore DNA sequencing is…What does it mean to sequence a genome?

From: breakfreefromyourstandstill

Part of “Joe’s Answer Bag Week”

A-la kazaam! Watch me attempt to explain something very complicated using nothing but words …

Genomic sequencing is a super hot topic in biology these days, based on how cheap and easy it is becoming (relatively, anyway). It’s easy to forget that some people might not fully understand what that means. This will start out ridiculously basic, but let’s see if I can summarize this in just a few paragraphs:

Can you reconcile what a genome at least represents? It’s the nucleic acid information inside every cell (doesn’t matter if it’s a bacterium, a fungus or a human … or a virus) that encodes all the instructions for life (argue amongst yourselves whether viruses are alive). In humans, it is ~3.2 billion base pairs of DNA inside of a nucleus. Everything that a cell can and ever will/won’t do is written in the patterns of this 3.2 billion character string. If we want to know what something in the cell does, like an enzyme or a signaling protein, then we have to know what that enzyme or signaling protein is made of. If we look all the way back in the genome and read the order of DNA bases, it’s like reading an Ikea instruction manual and figuring out what crappy table it makes in the end without actually pulling out those little hex wrenches. It doesn’t always work perfectly that way, but you get the idea.

So genome sequencing is just reading the DNA sequence of all the base-pairs in a cell’s instruction manual. But we don’t read them from one end to another, because that’s impossible. Instead we read them in small pieces, and then use powerful computers to put the small pieces together.

How we make the small pieces that we read is where it gets really interesting. When the human genome was first sequenced, they basically randomly chopped it up using a tiny amount of starting material. Then they amplified it (made more of each piece) so that they could read it using less sensitive technology and stitch it back together on an Intel 486 running Windows 98. It was sort of like reading a sentence three times to make sure you get it exactly right. But when you amplify DNA, you introduce errors and you end up with something like a book with a typo on every page (or sometimes missing whole pages altogether). It was also super F-ing expensive to do it, and it took ten years.

Since then, biology has been trying to make the process of reading DNA sequences cheaper, faster, and requiring less starting material. Nanopore sequencing is the newest and most bang-pow hotshot method that anyone’s invented. 

Imagine you are sitting on a sheet full of holes. The holes are just barely big enough to fit a strand of DNA through. Up through the middle you start pulling a single, tiny DNA strand, like thread through a needle’s eye. Thanks to your expert vision and extremely advanced biology knowledge, you can recognize each of the four DNA bases as you pull the string through, one-by-one. You copy them down on a piece of paper next to you, and pretty soon you’ve read an entire string of DNA, much longer than you could have with old technologies. That’s nanopore sequencing. It’s pulling a single strand of DNA through a tiny hole that reads every base as it passes by.

If you have thousands and thousands of those tiny holes, you can put together an entire genome from a bunch of single molecules, using powerful computers. It’s fast, cheap and it (hopefully) doesn’t have the gaps and typos that old-school sequencing does. Sequencing an entire genome could now take as little as a day, and for less than a few thousand dollars.

FOR MORE: Check out this post and this post to see some cool videos and stats about nanopore sequencing.

Nanopore DNA Sequencing

Does that mean anything to you? It should. People who know me know that I am prone to hyperbole (e.g. “This is the best freakin’ sandwich I have ever had, like, in history”), but believe me when I say that This. Changes. Everything.

Critics of genomics (even Craig Venter, “Mr. Genome” himself) have lamented the fact that sequencing our genome has not resulted in discovering the genetic basis of every disease. We have learned that human biology is orders of magnitude more complicated, redundant and networked than we ever imagined. But many people (including me) believe that we will only learn what we need to by sequencing more genomes.

Technologies like Oxford Nanopore’s, should they live up to their promises (or even half their promises), will make genome sequencing so cheap and so fast, that we will no longer be limited by how much genetic data we can assemble, only what we can process.

We will have to make sure that this doesn’t get applied to medicine all willy-nilly (true personalized medicine is still far-off), and watching for genomic snake oil hucksters will fall on all of our shoulders (they should be tarred, and then feathered). Kids: study that computer science. We’re gonna have a LOT of data to analyze.

I MEAN SERIOUSLY! THEY MADE A GENOME SEQUENCER THE SIZE OF A USB DRIVE THAT COSTS LESS THAN $1,000!! I’M LOSING MY MIND HERE!

Previously: Genome sequencing facts

(via Oxford Nanopore on Vimeo, for more check out Nature News)

Source: vimeo.com

Where we came from:
  • 10 YEARS: The amount of time that it took to sequence the first human genome, at a cost of $2.7 billion.
  • 9.5 YEARS: The amount of time that it would take you to read the human genome, continuously, were it printed in a book. Oh, and that book would be the size of 200 Manhattan telephone books.
  • 3 GIGABYTES: The amount of computer storage that one human genome takes up.

Where we are going:

  • 15 MINUTES: The amount of time that Oxford Nanopore’s new single-DNA strand reading technology would take to sequence the human genome.
  • $900: The cost of their smallest nanopore genome sequencer (not quite big enough for a human genome, but still). Oh, and it’s the size of a USB drive.

More coming tomorrow. This is a big deal. I love science.