Science science

Scientists edge closer to creating a blood test that can detect multiple types of cancers, seeing success rates of around 70% in cancerous individuals

Scientists edge closer to creating a blood test that can detect multiple types of cancers, seeing success rates of around 70% in cancerous individuals
Scientists edge closer to creating a blood test that can detect multiple types of cancers, seeing...

Interestingly, the tests detected Ovarian cancer 98% of the time, so that's not bad..

Ovarian cancer is so fatal because of the lack of screening options. By the time symptoms appear, it's often too late. As a person with a mutated gene that gives me a high risk of OC, the thoughts of having this blood test available makes me so happy

A 30% false negative rate seems high.

Basically: have someone find it while prodding inside you (if it's big enough), detect a lump by putting an ultrasound probe into your vagina (if it'sthe lump is big enough) or a bloodtest with more false-positives than real ones.

EDIT: unfortunate phrasing...

Hi! We’re here to talk about all things CRISPR and NIH’s Center of Excellence in Genomic Science. We’re researchers from Jennifer Doudna’s lab at UC-Berkeley and program directors from the National Human Genome Research Institute, part of NIH. Ask us anything!

Hi! We’re here to talk about all things CRISPR and NIH’s Center of Excellence in Genomic Science. We’re researchers from Jennifer Doudna’s lab at UC-Berkeley and program directors from the National Human Genome Research Institute, part of NIH. Ask us anything!

The Doudna lab's research on CRISPR biology led to the 2012 discovery of the mechanism by which small RNAs direct the protein Cas9 to bind and cut specific DNA sequences within cells, thereby altering a chosen DNA sequence and changing the cells’ activity in a programmed way. This work opened up a world of possibilities by providing a simple and effective means of making targeted changes in the genomes of virtually any cell type or organism. By supporting this research, the NIH is achieving its mission to advance the promise of genomic medicine through the precise manipulation of genes at a scale and level of accuracy that is not currently realized.

The National Human Genome Research Institute (NHGRI), part of NIH, has awarded a five-year grant to to the Doudna lab to establish the Center for Genome Editing and Recording as part of the Center of Excellence in Genomic Science (CEGS) program. The Center is pursuing two technological goals: 1) the improvement of the CRISPR technology to enable more efficient, rapid and accurate genome alterations; and 2) the implementation of robust readout technologies to quickly and accurately assess natural gene variations, as well as the success of CRISPR gene editing. In addition to work through the new Center, research efforts in the Doudna lab include discovering the mechanisms of novel Cas proteins and exploring new anti-CRISPRs which protect self DNA from CRISPR cleavage.

Our goal is to harness the power of CRISPR to benefit humankind by curing disease and caring for the environment. We’d love to hear your questions about this technology and the new Center of Excellence in Genomic Science. Ask us anything!

Your hosts today are:

Jennifer Doudna, Ph.D., Professor of Chemistry; Biochemistry and Molecular Biology at the University of California, Berkeley and members of her lab

Lisa Brooks, Ph.D., Program Director in the Division of Genome Sciences at NHGRI

Dan Gilchrist, Ph.D., Program Director in the Division of Genome Sciences at NHGRI

Lu Wang, Ph.D., Program Director in the Division of Genome Sciences at NHGRI

Carolyn Hutter, Ph.D., acting Division Director in the Division of Genome Sciences at NHGRI

Lawrence Brody, Ph.D., Division Director in the Division of Genomics and Society at NHGRI

Nicole Lockhart, Ph.D., Program Director in the Division of Genomics and Society at NHGRI

Mike Smith, Ph.D., Program Director in the Division of Genome Sciences at NHGRI

Relevant links:

Learn more about the Center of Excellence in Genomic Science (CEGS) program: https://www.genome.gov/10001771/centers-of-excellence-in-genomic-science/#al-4

Learn more about Dr. Doudna’s research: http://rna.berkeley.edu/

UPDATE: Hi Reddit-ers! We're wrapping up for today, but thanks for all the great questions! We're thrilled and honored that you find CRISPR science as cool as we do! If you want to see/hear more, Dr. Doudna will be live-streaming a chat with Siddhartha Mukherjee, author of the book, The Gene today at 4:30-6 pm PT. See the event here! https://www.facebook.com/igisci/

How concerning is the recently published finding that CRISPR-cas9 faces antibody resistance in humans? Is there a good workaround?

Thanks so much for coming to talk with us!

There has been a lot of discussion of potential catastrophic risks of misuse of CRISPR. Which risks do you think are the most over-hyped, and which do you think deserve more attention?

Dr. Doudna. We’re a group of undergraduates from the University of Maine Presque Isle and Fort Kent campuses attending an INBRE “Genome Engineering with CRISPR/Cas9” course. We’d love if you can address any of the following three questions:

Gene editing with CRISPR now seems simple and straightforward. To treat disease the real hurdle is cell-specific delivery of the editing machinery. What new advances are being made on this front?

We grow a lot of the world’s potatoes here in Northern Maine and are very aware that things like potato viruses cost our state millions each year. In theory, CRISPR can fix this, so should we give it a shot?

Anti-CRISPRs are an exciting new discovery. Can you speak on their potential to improve CRISPR-based treatments?

Hi, this is Kevin from the Innovative Genomics Institute. One potential misuse of CRISPR gene editing technology would include the release of gene edited organisms into the wild Gene Drives. This poses the risk of impacting fragile environments in unpredictable ways. Organisms can also cross international boundaries, which poses diplomatic risks. I think this risk deserves plenty of attention. One risk that is over-hyped is editing viruses to become hyper-infective and virulent. I think this is over-hyped because viruses quickly evolve and any modification may quickly be removed.

500 years later, scientists discover what probably killed the Aztecs. Within five years, 15 million people – 80% of the population – were wiped out in an epidemic named ‘cocoliztli’, meaning pestilence

500 years later, scientists discover what probably killed the Aztecs. Within five years, 15 milli...

The way I've heard it described, the Americas were colonized after a local apocalypse.

Imagine: You live like five hundred years ago, in a flourishing society. You have large cities, long distance trade, some dope monuments. All kind of cool plants have been domesticated like tomatoes, corn, potatoes, peppers, and all kinds of fruit. Things are pretty good.

But then that all starts to change. You start heading strange tales of fallow pale giants. They come across the sea on great boats, wearing metal armor that glistens in the sun and good deathly red by firelight. They wield powerful weapons, arms that bark out fire and spit death at a distance. Horrid tales of their encounters with distant clans begin to spread. But that's not all. Wave after wave of pestilence washes across the land. If you lucky enough to survive, you aren't unscathed. You likely lose family members, and definitely see friends and neighbors perish.

Cities become depopulated. Nineteen out of twenty are claimed. Trade breaks down. Famine ravages the land, be as the farmers are wiped out early on. Starvation makes survivors all the more vulnerable to the next plague. Alliances are severed. Some tribes are wiped away completely, or are so diminished that they're absorbed into neighboring groups.

And then it happens. Great ships begin landing, more and more frequently. They belch forth foreigners who spread like a new plague. They overrun the land and displace or assimilate nearly everyone that's left.

Edited for accuracy.

4000 a day on the low side 12000 on the high side,those people must have truly thought the world was ending and in a way it was.

Not 3 out of 4; 19 out of 20. both contemporary reports and archeology confirm that figure.

The Plague killed 1 out of 3 Europeans, and people stopped farming because they thought the world was going to end. Some historians say that it shook people's faith in God enough that it brought about the Renaissance.

Imagine what it was like when 19 out of 20 died. Bodies littered the ground because there was no one left to move them from where they fell. People converted to Christianity because they thought their gods had abandoned them.

For reference, Mexico didn't return to its pre-Columbus population until the 1880s.

Also just the sociological outcomes are nothing to sneeze at: People started joining death cults, gave up religion, everyone was pretty massively rich so many didn't work, instead partying and hedonism, and so forth. Imagine having most of your family die, and everyone you know has most of their family and friends die at the same time. Everyone is in serious mourning and dealing with the pain in various ways that are not too healthy.

A study found that 90% of patients who had "penicillin allergy” on their charts weren't actually allergic. The authors say many patients are getting broad-spectrum antibiotics (e.g. clindamycin) for no reason, which raises health care costs and makes antibiotic-resistant bacteria harder to treat.

A study found that 90% of patients who had "penicillin allergy” on their charts weren't actually ...

The problem is that no one sits patients down and explains what an allergy to medication is and how it differs from an intolerance or more likely a coincidental unpleasant experience. Health care workers just assume that patients know what they know and don’t/can’t take the time to explain. With the ease of access to information we would think that ignorance to basic medical knowledge would be less of an issue but it seems to be more and more of an issue.

I probably fall into that category. All I know is going to the doctor as a kid and they said I was allergic to penicillin. I've carried that info into my adult life. No idea if I really am or not.

See, with me, I have to answer "I don't know, I was given penicillin when very young and for every doctor's visit I can recall my mother simply told the doctor I was allergic to penicillin."

Every day at my job:

Nurse: Are you allergic to anything?

Patient: No only cats

Patient: Oh and I'm allergic to penicillin

Nurse: And what happens if you take penicillin?

Patient: I get a bad stomach

Nurse internally tries not to murder paitent

Science AMA Series: I'm Steven Strogatz, a professor of mathematics at Cornell University in Ithaca, New York. I apply math to biology and physics and love communicating with the public about math through books, radio shows, and New York Times articles, and I’m here today to talk about it. AMA!

Science AMA Series: I'm Steven Strogatz, a professor of mathematics at Cornell University in Ithaca, New York. I apply math to biology and physics and love communicating with the public about math through books, radio shows, and New York Times articles, and I’m here today to talk about it. AMA!Hi Reddit! I’m Steven Strogatz and I’m the Jacob Gould Schurman Professor of Applied Mathematics at Cornell University, New York. I have broad interests in applied mathematics. At the beginning of my career, I was fascinated by mathematical biology and worked on a variety of problems, including the geometry of supercoiled DNA, the dynamics of the human sleep-wake cycle, and the collective behavior of biological oscillators, such as swarms of synchronously flashing fireflies. In the 1990s, my work focused on nonlinear dynamics and chaos applied to physics, engineering, and biology. Several of these projects dealt with coupled oscillators, such as lasers, superconducting Josephson junctions, and crickets that chirp in unison. In each case, the research involved close collaborations with experimentalists. 

I enjoy branching out into new areas, often with students taking the lead. In the past, this has led us into such topics as mathematical explorations of the small-world phenomenon in social networks (popularly known as “six degrees of separation”), and its generalization to other complex networks in nature and technology; the role of crowd synchronization in the wobbling of London’s Millennium Bridge on its opening day; and the dynamics of structural balance in social systems.

I’m here to answer questions about a recent paper my group published in the journal eLife (https://doi.org/10.7554/eLife.30212; plain-language summary: https://doi.org/10.7554/eLife.30212.002) – where we used a simple mathematical model to discover why diverse infectious diseases and cancers show similar distributions in their incubation periods – or queries related to anything about mathematics and its applications more broadly. I’ll start answering questions at 1pm EST. AMA!
Science AMA Series: I'm Steven Strogatz, a professor of mathematics at Cornell University in Ithaca, New York. I apply math to biology and physics and love communicating with the public about math through books, radio shows, and New York Times articles, and I’m here today to talk about it. AMA!

I’m Steven Strogatz and I’m the Jacob Gould Schurman Professor of Applied Mathematics at Cornell University, New York. I have broad interests in applied mathematics. At the beginning of my career, I was fascinated by mathematical biology and worked on a variety of problems, including the geometry of supercoiled DNA, the dynamics of the human sleep-wake cycle, and the collective behavior of biological oscillators, such as swarms of synchronously flashing fireflies. In the 1990s, my work focused on nonlinear dynamics and chaos applied to physics, engineering, and biology. Several of these projects dealt with coupled oscillators, such as lasers, superconducting Josephson junctions, and crickets that chirp in unison. In each case, the research involved close collaborations with experimentalists.

I enjoy branching out into new areas, often with students taking the lead. In the past, this has led us into such topics as mathematical explorations of the small-world phenomenon in social networks (popularly known as “six degrees of separation”), and its generalization to other complex networks in nature and technology; the role of crowd synchronization in the wobbling of London’s Millennium Bridge on its opening day; and the dynamics of structural balance in social systems.

I’m here to answer questions about a recent paper my group published in the journal eLife (https://doi.org/10.7554/eLife.30212; plain-language summary: https://doi.org/10.7554/eLife.30212.002) – where we used a simple mathematical model to discover why diverse infectious diseases and cancers show similar distributions in their incubation periods – or queries related to anything about mathematics and its applications more broadly. I’ll start answering questions at 1pm EST. AMA!

How much did Ed Lorenz’ seminal work on chaos theory influence you personally?

How quickly did applied mathematicians in other fields pick up on his ideas? Were the consequences recognized immediately?

P.s. On behalf of graduate students everywhere, thank you for your textbook on chaos and nonlinear Dynamics.

This AMA is being permanently archived by The Winnower, a publishing platform that offers traditional scholarly publishing tools to traditional and non-traditional scholarly outputs—because scholarly communication doesn’t just happen in journals.

To cite this AMA please use: https://doi.org/10.15200/winn.151602.20659

You can learn more and start contributing at authorea.com

Yes! I'm glad you asked. For the past year I've been writing a new book, tentatively titled "The language of the universe". It's the story of calculus – how it was discovered, who discovered it and why, what they were hoping to achieve, and how calculus has helped make the world modern. I know that lots of students take calculus and learn how to do derivatives and integrals, but many have trouble seeing the point of it all. Unless a student goes on in science or engineering, the usual advanced placement course in calculus could seem like a pointless exercise. That course is usually taught in such a rush (because there is so much to cram in for the exam) that there isn't much time to learn about why the subject was created or what amazing things it has done for the world. In this new book, I'm trying to tell the stories and big ideas behind calculus. I want people to see that calculus is truly one of the greatest inventions and works of art that humanity has ever come up with. The book should be out sometime in 2019. Stay tuned!

Khan academy is free. There is math from kindergarten all the way up to multivariable calculus and differential equations.

Scientists Discover Clean Water Ice Just Below Mars' Surface

Scientists Discover Clean Water Ice Just Below Mars' Surface

I always see stuff like this (about detecting water or possibilities of it) on other planets but it never ends up being conclusive/important. I wonder if this would be different, considering that it's Mars.

Wow this ice is at over 55 degrees of latitude away from the equator which is where we would like to be living for heat reasons. Imagine having to get water from over 500 miles from where you live.

Edit: a bunch of people are saying “ya but oil” Or “I live in california broooooo that’s how we hella roll”

It’s pretty different.... there’s oceans, theres rivers, and there’s a couple hundred years of infrastructure built here on earth. Think about the capital cost of building a pipeline here... now think about trying to do it on Mars. It’s not trivial. Plus it’s cold and water doesn’t flow that well when it’s under 0 degrees. Best solution I’ve heard thus far is Ice Road Truckers 2: Mars edition, let’s just hope the history channel is still around.

*also km, my bad

More on the specifics. This frozen water was very pure, found in "temperate" latitudes between the equator and the poles, and extends more than 300 feet below the surface in some parts. Researchers have detected water ice on the surface of Mars many times, but this is a rare glimpse into the vertical structure of the ice deposits, which may allow scientist to study the layers and learn about the history of Mars climate.

Imagine living 34 million miles away from where you live right now.

I would like to think if we can move people in mass that far, we can move water 500 miles as well.

'Hypatia' Stone Contains Compounds Not Found in the Solar System. The mysterious Egyptian rock contains mico-mineral compounds not found on Earth, in any meteorite or comet, or elsewhere in the solar system.

'Hypatia' Stone Contains Compounds Not Found in the Solar System. The mysterious Egyptian rock co...

This is the first I have heard of this and really is one of the most curious things to me. This is the most "alien" thing we have on this planet and yet not much is talked about it to my knowledge. Really neat.

Anyone would think a meteorite would be cool today, so imagine how these people who believed in Gods who interact with them through nature seeing a ball of fire crash. It’d be seen as a godly item. I’m aware King Tutankhamen also had a dagger made of meteoric iron.

http://www.history.com/news/researchers-say-king-tuts-dagger-was-made-from-a-meteorite

I'm thinking the same thing. Why is this not more publicized? I wanna know more!

Technically they are found on Earth...

Ants can sense a chemical cue from other colony members with a fungal infection and respond by spraying them with an antiseptic poison that kills both the ant and the fungus inside.

Ants can sense a chemical cue from other colony members with a fungal infection and respond by sp...

Interesting, though I think it's slightly important to note that the ants can sense chemical markers from pupae that are infected (not adults), removing the pods they're growing in and injecting a fungicide.

The way the title is worded, I initially thought it applied to adult ants removing "infected" adult ants.

Doesn't really apply to an individual ant in a colony.

So they quarantine and burn the infected, got it.

Survival of the fittest

Scientists have now discovered that an alien stone contains exotic micro-mineral compounds not found anywhere on Earth or on any meteorites or comets – these compounds are in fact found nowhere else in the entire Solar System.

Scientists have now discovered that an alien stone contains exotic micro-mineral compounds not fo...
Scientists have now discovered that an alien stone contains exotic micro-mineral compounds not fo...

So it's not misleading, the abstract postulates that this rock's differences are because it originates in the pre-solar nebula, not that it came from another star system altogether. So the uniqueness is likely more due to age and timeframe of its formation than distance.

Didn't know they checked every rock in the Solar System.

Op editorialized this a lot more than the authors did:

A lack of silicate matter sets the stone apart from interplanetary dust particles and known cometary material. This, along with the dual intermingled matrices internal to it, could indicate a high degree of heterogeneity in the early solar nebula.

The authors are saying this came from the solar system and that it provides evidence that the early solar system (when it was a nebula) was highly heterogeneous (there were many different types of materials).

Try one of these subthreads