Nature Podcast

Introduction

This is a transcript of the 18th June edition of the weekly Nature Podcast. Audio files for the current show and archive episodes can be accessed from the Nature Podcast index page (http://www.nature.com/nature/podcast), which also contains details on how to subscribe to the Nature Podcast for FREE, and has troubleshooting top-tips. Send us your feedback to mailto:podcast@nature.com.

Kerri Smith: Coming up this week, the making of the Colorado Plateau.

Mousumi Roy: We know that something like 65 million years ago much of the region of the Colorado Plateau was at or near sea level and today these rocks are above sea level by as much as 3 or 4 kilometres, so something moved these columns up.

Adam Rutherford: And the importance of packaging.

Bradley Cairns: Many genes that are important for the development of the embryo are actually packaged and marked in a special way all the way back in the father's sperm.

Adam Rutherford: This is the Nature Podcast I'm Adam Rutherford.

Kerri Smith: And I'm Kerri Smith.To kick off this week, when it comes to DNA the packaging might be just as important as the contents. Here's Natasha Gilbert.

Natasha Gilbert: DNA in human sperm is wrapped much more tightly than it is in other types of cells. This allows sperm to take a much more stream lined shape for swimming, but a smaller portion of sperm DNA is not packaged so tightly, Bradley Cairns of the Howard Hughes Medical Institute in Maryland and his colleagues wanted to know why. When they looked into it they found that the genes packaged differently to the rest are important for embryo development. I called Bradley to find out how the discovery could help couples with fertility problems. Nature advance online publication (14 June 2009)

Bradley R. Cairns: So the long term role of the work is to create a clinical diagnostic test that will tell the difference between a sperm that is healthy and capable of making a healthy pregnancy and one that is not capable so that we can inform couples that are having problems with fertility about their prospects for having a healthy child and what we found is that many genes that are important for the development of the embryo are actually packaged and marked in a special way all the way back in the father's sperm. And we believe that this special packaging is going to be important for the expression or use of those genes at the right time in the right place in the developing embryo.

Natasha Gilbert: So what is so special about the ways sperm DNA is packaged?

Bradley R. Cairns: Well, other investigators have determined that the sperm genome undergoes an extensive repackaging as part of making a mature sperm. So the sperm DNA has to be packaged much, much more tightly than the DNA in a normal cell and the reason is that this is only cell in the human biology that has to swim and needs to make its head very small so it can swim quickly; so it uses a special molecule called protamine which wraps the DNA very, very tightly. And what we knew is that and what others have discovered is that this molecule protamine wrapped about 95 to 96% of the human genome; but about 4% of the genome was still retained in an alternative packaging molecule the one that is used in all of your other normal cells called histone. And we asked a very simple question that 4 or 5% of histone that remains in the genome in sperm cells is it simply randomly distributed with no function or is it localized at particular genes of importance and indeed we found it significantly enriched that these genes that are importance for guiding the embryo's development.

Natasha Gilbert: And what does this packaging protein do? What effect does it have on sperm DNA?

Bradley R. Cairns: Right we don't think that this protein has an effect on the sperms, the idea is that you put this protein on those genes solely for the purpose of helping those genes be expressed in the embryo. And it's not just a generic, a histone protein that's present on these important genes, it's a histone protein that has special chemical tags called modifications and there are different kinds of modifications that are present on histone proteins and one can think of them, of the different modifications, as sort, of green light, yellow light and red light that instruct the cell's machinery whether to express those genes at a certain time or at certain strength and what we found is that that sort of, lighting system is probably a very helpful in telling the embryo at what time to turn those genes on.

Natasha Gilbert: And so is it that the packaging of the genes in the sperm that's the most important thing for fertility?

Bradley R. Cairns: Well, at this point, we know that we have a very strong correlation between packaging and these genes. To show importance, you have to have very, very good correlations between the packaging state and fertility outcomes and that we don't have yet, so that's going to require probably a several year study where we assess the packaging status in probably thousands of patients and then look at their outcomes and make correlations and then derive a probability of success for the patients and also for us in terms of predictability.

Natasha Gilbert: What can this tell you, how can this help couples that are struggling with fertility?

Bradley R. Cairns: Yeah, that's a very good question. So the paper that we published, it solely examines the packaging state of fertile men, men of known fertility who essentially are positive controls, they have had many successful pregnancies in the in vitro fertilization clinic. So what we are looking at now is whether infertile men have incorrect packaging and we have preliminary evidence that that is true that a large percentage of men who have these fertility problems indeed have problems in packaging. And with all this we create a clinical diagnostic for packaging for one of two purposes, so even infertile men, many of them will have a small percentage of their sperm which are actually healthy and by developing this test, we might be able to separate out those that are the healthiest and therefore have the best chance of causing a healthy pregnancy. The second thing is that there may be cases where some of those infertile men have very severe problems in packaging and have in essentially no healthy sperm. And then I think it's important for the couples to know that the man has a very little chance of being able to have a successful pregnancy and the couples can consider adoption rather than these very expensive and you know emotional procedure of doing in vitro fertilization.

Adam Rutherford: Bradley Cairns talking to Natasha. In just a moment she will be back just like the terminator with the rum tale of science fakery, but first Geoff has been taking a jolly turn around the Colorado Plateau finding out how it got to be so high and so flat.

Geoff Brumfiel: The Colorado Plateau stretches across over 300,000 sq kilometres of the south western United States. It is flat and it is high and it is also home to some of the most beautiful landscapes in US including the Grand Canyon. But exactly how it got there has been something of a mystery to scientists. Normally you would expect tectonic plates to be involved, but the nearest plate boundary is around 1000 kilometres away along the Californian coast. Mousumi Roy works at the University of New Mexico in Albuquerque which sits just on the plateau's eastern edge. I called her to get her new theory on how it got there. Nature 459, 978–982 (18 June 2009)

Mousumi Roy: The Colorado plateau is a region that's elevated with an average elevation of about 2 km or so. Driving across the Colorado plateau one encounters landscape that's formed by the action of erosion and uplift of rocks and this landscape gives some pretty dramatic forms.

Geoff Brumfiel: What makes it so interesting, I mean, I guess from a geological standpoint, you've described how beautiful it is, but why would geologists take an interest in essentially a very flat piece of land without a lot of activity, right?

Mousumi Roy: That's right, so we know that something like 65 million years ago much of the region of the Colorado plateau was at or near sea level and today these rocks are, in some cases, above sea level by as much as 3 or 4 kilometres so something moved these columns up. One way in which rocks get moved up above sea level is if you shorten or squish a piece of the plate; say for example in the Himalayas rocks are continually being moved up above sea level because the Indian plate and the Eurasian plate are colliding. In the Colorado plateau there is evidence for the rocks having moved upward by you know not an insignificant amount, 2 km is a pretty large average rock uplift and yet there is not much evidence for structures, faults and folds and things that are large enough that could have accommodated that uplift.

Geoff Brumfiel: So, you've sort of come around to a different idea about how the uplift occurred and it has to do with warming of the lithosphere, is that right, the rock under the plateau.

Mousumi Roy: Yes, our model proposes that the main mechanism for uplift of the rocks of the Colorado plateau is some sort of thermal modification of the plate by processes that happen since 65 million years ago. The way that our thermal expansion model differs from you know previous ideas of thermal effects is that we specifically tiered two processes that involve the removal of the Farallon plate from beneath North America. At a subduction zone, two plates come together and one of the plates sinks underneath the other plate into the mantel.

Geoff Brumfiel: So what's the Farallon plate exactly and what does it have to do with this story?

Mousumi Roy: So the western boundary of North America have had a long history of subduction and what's happened is since at least 80 million years or so, we had subduction going on where a plate which is now no longer at the surface called as Farallon plate actually sink underneath the western part of the US.

Geoff Brumfiel: So what happened to the plate, I mean, it literally sink without a trace?

Mousumi Roy: Well, the key here is that around 40 million years ago, we think it got removed from beneath the Western US and so beneath the Colorado plateau and one thing that that does is it may provide a thermal perturbation to the base of the plate, so while the plate was being underlain by the sinking Farallon slab, the Farallon plate is very cold and dense and so you know it would have refrigerated the mantle directly above it so the base of North America would have been relatively cold. Once you remove the Farallon plate you bring hot asthenosphere which is you know flowing mantle, into contact with the base of North America and you suddenly heat up the base of the plate.

Geoff Brumfiel: That will cause then the Colorado plateau to, sort of, swell up like a boil or a blister I guess.

Mousumi Roy: Yeah, so one of the other things about the Colorado plateau is that we think it's a region where the plate itself is thicker than the surrounding regions. So the plateau is this region where the plate has, kind of I imagine it sort of like a protrusion, into the flowing mantle or some people might call it a keel where the plate is thicker and once you provide this thermal perturbation to this weird keel then you can actually drive warming of the keel and the warming proceeds not just by warming from below but because you have this keel-like shape it can actually warm from the outside inward and that's one of the key things about our mechanism for uplift of the Colorado plateau. We think that there has been this thermal modification of the plate from the outside end.

Geoff Brumfiel: So do you think that this is going to settle the debate then on the Colorado plateau or is this just going to be another model?

Mousumi Roy: So, I like this model because of simple and it explains a broad range of data, but like any model one has to accept that you, know, with time there will be refinements and or a complete rejection of the model, so I would be wrong to say that I thought that the debate is over, but certainly this model does, I think, a better job of explaining a really broad range of data and observation.

Kerri Smith: That was Mousumi Roy talking to Geoff.

Jingle

Adam Rutherford: The news rocket will be deployed in just a minute, blog Captain Dan Cressey is standing by, but before that you might think that we talked some nonsense on this show but how about this:Compact symmetries and compilers have garnered tremendous interest from both futurists and biologists in the last several years. The flaw of this type of solution however is that DHTs can be made empathic, large-scale and extensible. Along these same lines, the drawback of this type of approach however is that the active networks and SMPs can agree to fix this riddle.That's the opening line of a paper submitted to a publication called The Open Information Science Journal, but all is not quite how it seems. Natasha Gilbert has been watching this story unfold and she is here in the studio to tell us about this hoax. Natasha, start from the beginning. Published online (15 June 2009).

Natasha Gilbert: Okay, well a guy called Phil Davis who is a graduate student in communications studies at Cornell University in America. He had been receiving e-mails requesting him to submit articles to this publisher called Bentham Science Journals and so it made him a little bit, he asked himself a question you know what would happen if I sent in a fake paper, would they accept it. Because this is an open access journal and you have to pay to publish your articles in that so he did that. He created a computer generated paper which is absolutely nonsense and they accepted the paper which and at that point the publishers asked him to pay around 800 US$ to have that article published.

Adam Rutherford: So, just to be clear on this, this is a standard new publishing model that companies like the Public Library of Science and this other Publisher Bentham are using, where the author of a scientific study actually pays to have that paper published in their journal and it becomes free to the people who are reading it, right?

Natasha Gilbert: That's right that's one of the models that open access publishing uses. It's not the only model, but one of the models that they do use yep.

Adam Rutherford: So Bentham the publishers of this journal accept this fake paper for publication and then what?

Natasha Gilbert: At that point, Phil decided to well, you know, he said that he was going to retract the paper because obviously it was fake and he did not want to go any further but he then went public with what had happened and this has caused you know a huge stay on the blogosphere and in the news.

Adam Rutherford: Okay, so we know very well at Nature that the standard publishing procedure is an author submits a study and then our editors send it out to peer review, which is other scientists in the same field look at it anonymously and determine and advice on whether that paper should or should not be published or should be revised or should be rejected. Now can you just describe the process that happened with regards to this fake paper as it went to the journal in question?

Natasha Gilbert: At the moment, it is not entirely clear. I spoke to the editor of the journal that accepted the fake paper, his name is Bambang Parmanto, he is an information scientist at the University of Pittsburgh and he told me that he had absolutely no knowledge of the paper before it was accepted by the journal. He had not seen it and he had not seen any of the reviewer's comments. He told me, the editor told me that when he spoke to the publishers to find out what was going on, they told him that one person on the journal's editorial board had reviewed the paper. Nature contacted the publishers; they told us in a statement that, two peer reviewers had looked at the paper and that they knew that it was a fake and the reason that they accepted the paper was to try unearth who had sent it in.

Adam Rutherford: Now you just heard a clip from the paper and it's pretty obvious that it is gibberish as it is randomly generated but they also had another reason for thinking that it was fake, right?

Natasha Gilbert: Yeah, the publishers say that they had previously received a fake paper which they rejected and this paper was also sent in by Philip Davis, it's probably important to know that both of these papers were sent in under pseudonyms and under different pseudonyms. But Phil told me that in fact the second fake paper which was rejected by the publishers was sent in after the first fake paper.

Adam Rutherford: So there was certainly some inconsistencies in this story, so what happened next?

Natasha Gilbert: Well when I spoke to the editor Bambang Parmanto who is actually also a working scientist at the University of Pittsburgh, he told me that the situation is unacceptable and that he will step down. He said, you know the peer review system did not work and that I quote "the publisher could take advantage of the fees and that's why I want to leave."

Adam Rutherford: So, this is a pretty major story for scientific publishing, have Bentham publishers responded yet.

Natasha Gilbert: Yes, they have, we sent them in some very specific questions they responded in a more general statement saying that their peer review policy is to have two peer reviewers looking at every paper and that they you know they still uphold that process and again, you know their justification for accepting the paper was that they wanted to unearth the people that had sent in the fake paper.

Adam Rutherford: Okay thanks Natasha, she is going to be following the story like a panther as it develops on http://www.nature.com/news.

Kerri Smith: And sticking with this week's news the blog master Dan Cressey is here and he has all the latest on swine flu first of all.

Daniel Cressey: Well, we now have the first death outside of the Americas and the World Health Organisation has officially upgraded us to pandemic level 6 which means we're now officially in a pandemic.

Kerri Smith: So two pieces of news that mean we should may be a bit more worried than we were before or?

Daniel Cressey: The upgrading of the pandemic level will probably not make much difference in practice to the efforts being made to stop H1N1, but it is significant that the WHO has finally decided this is officially a pandemic with what they call sustained community level outbreaks in two or more countries in two different regions of the world.

Kerri Smith: So that's the definition then. So this has gone from 5 to 6, how many levels are there?

Daniel Cressey: 6 is the highest level indicating that this is a full blown pandemic, so this is the first influenza pandemic for 41 years and the fourth this century with previous outbreaks being in 1918 and 1957 and 1968.

Kerri Smith: Do you know much about how this current one compares to those previous outbreaks, I mean 1918 was pretty severe?

Daniel Cressey: At the moment that the WHO states this is a moderate pandemic and it is not on the level of the infamous 1918 outbreak but it could get worse.

Kerri Smith: And for more on the swine flu, there is a review appearing on the H1N1 virus in Nature this week, so check that out. Now the second story that you have brought us Dan is about some satellite data that is no more.

Daniel Cressey: That's right well the data itself is still there, but the scientists can't get to it anymore. My colleague Geoff Brumfiel has been reporting on this, this week. Astronomers used to be able to sneak a peek at incoming meteors using military surveillance satellites and they are not being allowed to do this anymore.

Kerri Smith: That seems a shame I mean these satellites are there to monitor nuclear tests and that kind of thing, aren't they on behalf of the US government, what were the scientists getting out of it?

Daniel Cressey: Well these satellites can measure infrared data, so what they can pinpoint was the time, location and brightness of any meteors as they were entering the Earth's atmosphere, which is obviously something that a lot of researchers are quite interested in.

Kerri Smith: So what's happened I mean, does the arrangements just come to an end?

Daniel Cressey: Well, the military has been quite tight lipped about exactly why they have stopped giving out these data, one suggestion is that they have launched a new generation of military satellites and it could just be too much hassle for them to chop out the data that scientists are allowed to see and the stuff that they want to keep hidden. Of course the more cynical explanation is that they don't want anyone to know quite how good these new satellites are.

Kerri Smith: So there must some pretty miffed scientists around, how do people feel about this?

Daniel Cressey: This data was quite unique; one scientist told Geoff that there was nothing else that even comes close to it.

Kerri Smith: And some news finally of a new discovery and a new element.

Daniel Cressey: That's true the International Union of Pure and Applied Chemistry who are the globe's top chemistry buffins have asked Sigurd Hofmann of Germany to pick a name for an element which he and his team have discovered, currently element 112 which has 112 protons in its nucleus has been given the holding name of ununbium or ununbium which might more classically educated what means, tell me, it's based on the Latin for 112 and not a very inspiring name.

Kerri Smith: But typically a name that a scientist might christen it with?

Daniel Cressey: True but professor Hoffmann is now going to have to come up with a rather better name, previous elements discovered at the same centre have been named after scientists that we have had Bohrium and Hassium and one was even named after the location in Darmstadt, Germany and is Darmstadium.

Kerri Smith: So is it going to be useful.

Daniel Cressey: Unfortunately, you can do pretty much nothing with this element as it disappears in an instant, so no new super metals for us.

Kerri Smith: Oh what a shame. Well thanks Dan for stopping by.

Daniel Cressey: Always a pleasure.

Kerri Smith: You know, go to http://www.nature.com/news and Dan's blog the Great Beyond also on the news site for more on those stories.

Adam Rutherford: That's almost it from us, next week we'll have the usual ridiculously exciting research and science news plus an act of confusing post modernism will be putting science journalism itself under the microscope. Till then I'm Adam Rutherford

Kerri Smith: And I'm Kerri Smith and to end the show this week, a biochemical ditty. Biotech professor Cliff Wang at Stanford University offered his class the chance to do an independent project as part of their biotech course and two students Lindsay Liebsen and Devin King penned and performed this tune. So consider this as a shout out for them and the rest of the class. Thanks Cliff, if like Cliff you would like to get in touch with us, send us an e-mail to mailto:podcast@nature.com.