The DNA Network |
| In your facebook [genomeboy.com] Posted: 18 Jun 2008 07:05 PM CDT Privacy is changing rapidly and in ways we can barely comprehend. Will we live our lives differently, fearing that our everyday social contacts are going to wind up in some great database? How will the world change when group photos snapped at parties all turn into misleading edges in that permanent, all-encompassing social graph? Can society limit the abuse of personal information without resorting to Internet censorship that would violate the First Amendment? Yes, already happening, and no. (hat tip) |
| 2007 Impact Factor [The Seven Stones] Posted: 18 Jun 2008 05:37 PM CDT
The Impact Factor of Molecular Systems Biology for 2007 is 9.954 This represents a substantial increase over last year's Impact Factor (see chart) and we would like to warmly thank all our authors and reviewers who have contributed to this success. We will continue to work very hard to maintain the high standards of the journal and promote innovative and insightful research in systems biology. The significance of Impact Factors suffers from intrinsic limitations (see Ian's post) and interpretation of this metric is subject to much discussion (Rossner et al 2007, Thompson's Citation Impact Forum). These and other questions related to bibliometrics are also currently debated at the Nature Network Citation in Science group. |
| How many genes do you share with your twentieth cousin? [evolgen] Posted: 18 Jun 2008 03:30 PM CDT John Hawks has an interesting post on what it means to be human in which he argues that our "human-ness" (humanity?) is our shared evolutionary history. I like it. But Hawks also writes the following:
I could share no genes with my twentieth cousin? This kind of sloppy use of terminology is not what I've come to expect from John. He's usually at his best when writing about human genetics. You see, the quoted statement could vary from true to wildly inaccurate depending on the definition of gene we're using. Read the rest of this post... | Read the comments on this post... |
| Investigating Selection on Viruses: A Statisical Alignment Approach [Mailund on the Internet] Posted: 18 Jun 2008 01:40 PM CDT Woohoo, we just got a paper accepted. Although it is at BMC Bioinformatics, it isn’t one of the papers I’ve been bitching about — this one we got very helpful reviews on. It is work from when I was in Oxford. Saskia de Groot did analysis of virus genomes for her PhD (see papers here and here) but for viruses that are relatively far divergent, getting good alignments is a bit of a problem, so I suggested we took a statistical alignment approach to integrate over the uncertainty. So we got together with Gerton Lunter — who does work with this — and came up with this:
I’ll add a link to the paper as soon as it is up at the journal. What’s the problem?We were trying to figure out selection in viruses where genes can have overlapping reading frames. In such cases, figuring out the neutral substitution rate is a bit of a problem, ’cause a synonymous substitution in one gene can be a non-synonymous substitution in an overlapping gene. Using dN/dS to figure out selection won’t work. Instead we took and extended a method by Hein and Støvlbæk to explicitly model substitutions with selection in overlapping reading frames. We ought to consider the neighbour dependent substitutions you get when you are modelling codon changes (which again is complicated by overlapping genes), but methods for that can be very slow and won’t scale to whole genomes. Even virus genomes. Pedersen and Jensen tried that in an MCMC approach. Hobolth’s recent approach might have worked — it is the paper I blogged about a little back — but we didn’t know about it at the time. Anyway, we essentially have a method for modelling the evolution over overlapping genes, but we cannot trust the alignment of viruses because they are too divergent, and if we infer an optimal alignment it is almost certainly wrong. An optimal alignment will often have too few substitutions compared to the real alignment. What did we do?Since we cannot trust a single alignment, we instead sum over all possible alignments. Using hidden Markov models, we can do that, and at the same time calculate the probability of any single one of them. We can then consider the substitutions in each of the alignments and weight the observed substitutions with the probability of the alignment. That way, the more likely alignment weigh in more when we consider substitutions than less likely. It is similar to what Rahul Satija, Lior Pachter and Jotun Hein were doing for phylogenetic footprinting in the neighbour office at the samme time… Using this approach, we show that we alleviate a systematic bias in using optimal alignments and get better estimates of selection factors. We only handle pair-wise alignments but hack our way out of using more sequences to get better estimates still. It isn’t really the best approach and we should probably try a Gibbs sampler to handle multiple sequence alignments, but that is left for future work… |
| Does Darwin Get Too Much Credit? [adaptivecomplexity's column] Posted: 18 Jun 2008 12:36 PM CDT At her NY Times blog, Olivia Judson looks at the upcoming year of Darwin celebrations (July 1, 1858 was when Darwin first presented ideas on natural selection, both his own and those of Alfred Russell Wallace, to the Linnean Society in London; Darwin's 200th birthday is coming up in February, and in November 2009 comes the 150th anniversary of the publication of On The Origin of Species - that's a lot of celebrating coming up), and asks, does Darwin really deserve all this credit? According to Judson, the answer is yes. But why, if Darwin wasn't the first to come up with the idea of evolution, and the concept of natural selection? Darwin may not have been the first, but ultimately he was the most persuasive:
In other words, to be a great scientist, you have to have good ideas, and persuasively communicate them to your colleagues. Darwin did this very well - the Origin is filled with detailed evidence from a variety of fields. On top of that, Darwin argued that his ideas were testable, and proposed tests that he himself and others could do. Darwin may not have been first to come up with all of the ideas presented in the Origin, but he was the first to really get evolution going as a healthy scientific field. And for that, the celebrations are justified. |
| Epigenetics News Returns [Epigenetics News] Posted: 18 Jun 2008 11:35 AM CDT In February 2008, I made the decision to shut down this blog in order to spend more time focusing on completing my degree and pushing my research project forward. Last month I completed my B.S. in Genetics and Cell Biology at Washington State University after an extremely stressful four years in which I tried to balance responsibilities as a full-time student, undergraduate researcher, husband, father, and blogger, among many other pursuits. This year, something had to give as my class schedule was extremely demanding and lab courses required a much larger share of my time. In addition, I had decided not to attend graduate school right away and was turning my attention to finding a research technician position in the area. That search is still ongoing, and I have applied for and interviewed with a number of research labs at WSU. It’s amazing how quickly you learn about other research programs under way when you begin to interview for positions. Many of the PIs hiring are working on newly funded grants that have not yet been publicly disclosed, and being able to get a glimpse of the work being done in a wide range of research areas has been a great educational opportunity. I have been working on a particular project for the last 3+ years (still ongoing), and it’s easy to become so immersed in your research that you forget about what others are doing around you. The job search has been a refreshing change of pace and I am looking forward to the next stage in my research career, whatever that may be. With that said, epigenetics research has continued to capture my attention over the past four months. This area of research has produced dramatic advances in our understanding of stem cells, cloning, cancer, development, nutrition, toxicology, and many other areas. With one educational milestone completed, it has opened up a space to continue to highlight important advances in epigenetics research at Epigenetics News. With some additional time available — and my newly acquired knowledge of important concepts and techniques critical to interpreting current research — I hope to make this project more of what I originally envisioned and present a more coherent view of the epigenetics research landscape. Thank you to all of you who offered your encouragement and support for this project, and especially to those that stuck around as RSS or newsletter subscribers while the site displayed abstracts. Welcome back! |
| How is math the basis of reality? [adaptivecomplexity's column] Posted: 18 Jun 2008 11:15 AM CDT "Most people will have a hard time accepting that their fundamental existence turns out to be the subject they hated in high school." Discover magazine has an interesting interview with MIT cosmologist/philosopher Max Tegmark, who argues that "there is only mathematics; that is all that exists." Tegmark's ideas the latest development in a line of thought that mathematicians, physicists and philosopher have been thinking about for years, millennia even. A good way to jump unto this subject is to read physicist Eugene Wigner's classic "The Unreasonable Effectiveness of Mathematics in the Natural Sciences." |
| Quack hunting season is open [Bayblab] Posted: 18 Jun 2008 10:21 AM CDT Apparently the FDA is going after quacks who are selling cancer "cures" over the internet. They sent letters to 25 of these outfits and may follow-up with seizures and criminal prosecutions. from the article: "The letters criticized unproven claims made about these products including the ability to "destroy the enzyme on DNA responsible for cancer cells," and the power to "neutralize" carcinogens. One product's Web site had a testimonial claiming it had cured a patient's skin cancer in three days, according to one of the letters. The ingredients of these unproven treatments include bloodroot, shark cartilage, coral calcium, cesium, ellagic acid, and a variety of mushrooms among other products." |
| Introgression of the yellow skin trait in domestic chickens [Yann Klimentidis' Weblog] Posted: 18 Jun 2008 09:32 AM CDT  Previous research on mtDNA has supported Darwin's hypothesis that domestic chickens are descended only from the red junglefowl. Here, they look at the ancestry of the domestic chicken at a locus (around the BCDO2 gene) that is associated with the yellow skin found on the legs of many domestic chickens. They find thatthe polymorphism is likely a tissue-specific regulatory mutation, and that it might have been picked up recently from the grey junglefowl. regarding the implications of what they find: In contrast, the minimal sequence divergence between the grey junglefowl BCDO2 sequence and the domestic yellow skin allele makes it highly unlikely that the divergence between the white and yellow skin alleles predates the speciation of the red and grey junglefowl; the Y sequence would have accumulated numerous sequence differences since the split between the red and grey junglefowl. We cannot exclude the possibility that yellow skin was introgressed to the red junglefowl by hybridization with grey junglefowl prior to domestication, but it is much more plausible that introgression was facilitated by human activities. The red and grey junglefowls are full species as demonstrated by the fact that hybridization does not occur in the wild [17] and when attempted in captivity, only a cross between grey cocks and red hens produced mostly sterile offspring [19]. Hybridization between grey junglefowl and domesticated fowl, however, have been reported in the vicinity of villages within the area of contact between the two wild species [17], suggesting that the introgression of yellow skin into domestic birds took place after chickens were initiallyThey mention that consumers in the US, Mexico and China prefer yellow skinned chickens ...interesting... , also: During lay, carotenoids are mobilized and deposited in the yolk of the egg. It is therefore worth speculating that the bright yellow skin color, expressed by well-fed yellow skin homozygotes but not by well-fed white skin birds, has been associated with high production and good health at some point during domestication and was therefore favored by early farmers. Of course, yellow skin may also have been selected purely for cosmetic reasons.Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken Jonas Eriksson, et al. PLoS Genetics Abstract: Yellow skin is an abundant phenotype among domestic chickens and is caused by a recessive allele (W*Y) that allows deposition of yellow carotenoids in the skin. Here we show that yellow skin is caused by one or more cis-acting and tissue-specific regulatory mutation(s) that inhibit expression of BCDO2 (beta-carotene dioxygenase 2) in skin. Our data imply that carotenoids are taken up from the circulation in both genotypes but are degraded by BCDO2 in skin from animals carrying the white skin allele (W*W). Surprisingly, our results demonstrate that yellow skin does not originate from the red junglefowl (Gallus gallus), the presumed sole wild ancestor of the domestic chicken, but most likely from the closely related grey junglefowl (Gallus sonneratii). This is the first conclusive evidence for a hybrid origin of the domestic chicken, and it has important implications for our views of the domestication process. |
| Prochlorococcus on Science Friday [The Tree of Life] Posted: 18 Jun 2008 09:32 AM CDT  Well, I wish I had known this in advance and I would have posted something about it here before last Friday. But anyway - Penny Chisholm (from MIT) and her beloved Prochlorococcus (important photosynthetic marine microbes) were featured on Science Friday last week. Fortunately, NPR broadcast's like ScienceFriday are a form of Open Access. And you can listen to Penny here. It makes for some good listening -- she has some good lines about the importance of microbes as well as the need for more support for work on microbes. She also gives a good plug for the Gordon and Betty Moore Foundation's Marine Microbiology Initiative (full disclosure - I just got a grant from this program). Note - the Science Friday host makes a bit of a blunder when at the end he asks if they have talked about viruses when a few minutes before she had done exactly that (for more on Prochlorococcus viruses see the Sullivan et al PLoS Biology paper here). You can also get a video of Penny giving a talk here. |
| Cat-fight over California [Genetic Future] Posted: 18 Jun 2008 09:14 AM CDT  A couple of days ago I mentioned California's regulatory smackdown of direct-to-consumer genetic testing companies, and the triumphant response of Helix Health's Steve Murphy to the news. Steve has long argued that physicians need to play a role in any genetic testing with potential health consequences - unsurprisingly, given that this is exactly what his business model depends on. California's regulatory response struck Steve as exactly what the doctor ordered: That's right, in order to test, you are soon going to have to document informed consent and evaluation by physician or extender. So anyone not doing what Helix Health is doing will soon find themselves on the wrong side of the law....again.Well, Steve's tone certainly got him some attention. In the comments to his post, Steve's response to the news was described as "rent-seeking" and "arrogant"; and today, Wired blogger Thomas Goetz criticises Steve's "paternalistic tone" and argues strongly against a physician-centred vision for the future of the personal genomics industry: Having been tested by both 23andMe and Navigenics, I can say that, yes, it's complicated. But frankly I don't need a doctor, and I don't want a doctor, to facilitate my understanding of what my DNA means.Deepak Singh from bbgm is similarly outraged by the regulators, given the ignorance of the average medico in matters genetical: This is my data and it's my decision. Regardless of what you think about the services and their utility or lack thereof, it's ludicrous to think that doctors, most of whom know less about genetics than I do, need to make a call on this. It's a personal decision. [my emphasis*]I naturally side with the freedom-of-genetic-information folks on this issue. As I said in my last post (in a comment that was echoed by David Ewing Duncan in Wired), what we're seeing here is to some extent a turf war, with the medical establishment trying to use legislation to claw back deference and power that used to be theirs automatically. Unfortunately for them, we're already living in a world in which people justifiably feel a strong sense of ownership over their genetic information; that's not going to change, and doctors will simply have to adapt to the new rules of play. However, at the same time I want to emphasise the dangers of heading too far in the opposite direction. Three hours reading the 23andMe website and Googling "type 2 diabetes" does not make you an expert on this disease. Seriously - they may not know what a SNP is, but when it comes to diseases doctors know stuff that you can't get from Google. Now, I don't believe that I should need a doctor's permission to sequence my own genome, and I see no need for laws compelling me to see one afterwards. Nonetheless, it is crucial that readers don't walk away from this discussion feeling that the medical profession is suddenly irrelevant to the shiny, high-technology era of health genomics. Clinicians will be absolutely critical when it comes to making personal genomics medically useful - or at least they will be once the medical establishment stops trying to make itself relevant through legislation, and instead focuses on providing doctors who are capable of engaging with genomic data. If they manage this, in a few year's time nearly every personal genomics customer will be reviewing their sequence data with a medical professional: not because the law says they have to, but because they want to. It's unfortunate that Steve's clear financial conflict of interest undermines his credibility here (as most of his critics have pointed out, some savagely) since his position is not baseless: clinicians do have an important role to play. He just needs to realise that brute legislative force is not the right way to achieve this end. * It's worth noting that the knowledge of genetics of most of the people commenting on this topic (certainly including Deepak) is waaaaay better than the average personal genomics customer - I think we all need to carefully calibrate our outrage to allow for the fact that the regulators are aiming at people who know much less about this stuff than the typical genetics blogger does. We should still be annoyed; just slightly less than we actually are.  Subscribe to Genetic Future. |
| Are You Intellectually Clean? [The Tree of Life] Posted: 18 Jun 2008 09:10 AM CDT Well, brain doping continues to be an issue, long after the buzz of April Fools Day is over. Now comes what I think must be a spoof of some kind: a site where people can make an "Academic Oath" saying they are clean by putting the following on their CV or WebSite: For the honour of humanity and the integrity of the academy, I declare I have not, nor ever will, use any drug for an intellectual advantage. See, www.academicoath.com |
| Finer mapping of European ancestry using personal genomic data [Genetic Future] Posted: 18 Jun 2008 08:20 AM CDT Dienekes has put together a neat little tool that uses variation data from either 23andMe or deCODEme to estimate whether a subject's ancestry stems mainly from Northwest European, Southeast European, or Ashkenazi Jewish populations, using a set of published markers that are strongly differentiated between these population clusters. There's more detail on how the tool operates here; to use it, you'll first need to download the R software environment from here. Like the Promethease tool, this is a great example of how the human genomics community can help genetic testing customers wring the most out of the rich, complex trove of data in their own genome. Subscribe to Genetic Future. |
| Posted: 18 Jun 2008 08:19 AM CDT In a recent post, I wrote about an article that I read in Science magazine on the genetics of learning. One of things about the article that surprised me quite a bit was a mistake the authors made in placing the polymorphism in the wrong gene. I wrote about that yesterday. The other thing that surprised me was something that I found at the NCBI. |
| Gone to the pups [genomeboy.com] Posted: 18 Jun 2008 08:00 AM CDT |
| Posted: 18 Jun 2008 07:22 AM CDT
Amidst his hectic schedule managing the ongoing credit crisis, the New York Times notes that Federal Reserve chairman Ben Bernanke opened a bipartisan symposium which will, “lay the groundwork for what leaders of both parties predict will be a major push for health care legislation next year.” From the article, it seems that since healthcare accounts for such a large (and growing) slice of the federal budget pie, fixing inefficiency and disparity in healthcare will assuredly involve more legislation and regulation on a growing scale. The article bummed me out since I suppose it portends new and shifting regulatory layers that will just make it harder for entrepreneurial consumer-driven and health2.0 innovations to establish themselves. Coincidental bummer that this symposium was taking place on the day NY and CA were stifling a new genetic testing industry. |
| Posted: 18 Jun 2008 07:13 AM CDT  The Peregrine Falcon is often called the fastest animal on earth, reaching speeds of up to 320 km/h during an aerial dive. It is also an example of successful conservation efforts. Widespread use of DDT severely affected the Peregrine population, putting the bird on the endangered species list. The chemical altered adult breeding behaviour, and its accumulation in bird tissues led to inadequate calcium and more fragile eggs. In the 70s, a DDT ban and conservation programs helped the bird make a comeback and in 1999 it was removed from the endangered species list. Today it enjoys 'least concern' status.One doesn't have to go far to see the Peregrine Falcon in the wild. While historically they built their nests on cliffs in coastal areas, they've also adapted to life in the big city. Replacing the cliffside with a highrise and with an ample pigeon population to feast on, the falcon is also at home in an urban setting. Here in Ottawa, a downtown nest can be found at the Crowne Plaza Hotel (Lyon Street) where they are monitored by the Ottawa Field-Naturalists club and the Ontario Ministry of Natural Resources. Two new chicks were hatched there earlier this month. |
| Alcohol Causes Cancer [Sciencebase Science Blog] Posted: 18 Jun 2008 07:00 AM CDT
Alcohol blamed for oral cancer risk - A large-scale statistical analysis of mouth and throat cancer incidence over a long period of time has looked at possible correlations between exposure to industrial chemicals, dust and alcoholic beverages in a wide variety of individuals in different occupations across Finland. The perhaps surprising conclusion drawn is that alcohol consumption rather than industrial chemicals or dusts is the critical factor associated with this form of cancer. Get the full story in this week’s edition of my SpectroscopyNOW column here. I suppose it’s a little ironic that in the same edition of Spec Now, I’m also writing about how to make beer taste fresher and last longer on the shelf. NMR spectroscopy, and a chromatography sniff test have yielded results that could help brewers improve the flavour and shelf-life of beer thanks to work by scientists in Venezuela. The team has identified alpha-dicarbonyls as important compounds that reduce beer’s flavour and point to a new approach to brewing beer that stays fresher, longer. Take a sip here… Meanwhile, another subject of mixed messages regarding health benefits is that perennial favourite chocolate. To maintain the seductive and lustrous brown gloss of chocolate, so enticing to chocoholics the world over, food technologists must find a way to prevent fat bloom from forming on the surface and turning the surface an unappealing grey. Now, scientists from Canada and Sweden have found new clues to understanding the microstructure of chocolate and what happens when it turns grey with age. More… Finally, some straight chemistry with absolutely no hint of biomedicine, health, or pharmaceutical implications (yet). A novel structure studied using X-ray crystallography hints at the possibility of a carbon atom that, at first site seems to be a little different from the conventional textbook view. Could the oldest rule of organic chemistry have been broken at last, or is low atomic separation being equated too keenly with the presence of a bond, or could there be something else afoot, as Steve Bachrach suggests? Read on… A post from David Bradley Science Writer |
| What does DNA mean to you? #10 [Eye on DNA] Posted: 18 Jun 2008 03:01 AM CDT
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| The Tree of Life: Freeing My Father's Scientific Publications Update [The Tree of Life] Posted: 18 Jun 2008 02:20 AM CDT Well, I have made some progress already in my quest I began on Father's Day to free up the scientific publications of my father (see The Tree of Life: Freeing My Father's Scientific Publications). I wrote to the powers that be at the journal "Endocrinology" asking about when back issues might be made available. And I got a VERY quick reply from someone from Highwire Press which is the place that puts out Endocrinology on the web Dear Jonathan Eisen,The person who wrote back was almost apologetic about how long this might take but I am personally very pleased. Given that Endocrinology says the make all articles more than a year old available for free, this likely means that my father's three papers in Endocrinology will soon be available for free online. This then changes my tally to: Pubmed Central: 3 Free access: 17 Fee access: 11 Unavailable: 4 Getting better. Of course, I want them all to be as widely available as possible so I am still going to work to move everything up the list towards Pubmed Central. Also, my brother suggests (in the comments to my previous post) that since my father was a government employee we should be able to just post his papers online. I think this is a good option but I still will be working on the "official" channels to see what happens. Since I made the original posting there have been some useful comments about what I might do on some other sites. See for example, this FriendFeed discussion (I have just discovered FriendFeed and it seems quite cool but I am not sure if everyone can see this discussion or not so please let me know if this link does not work). I will keep posting on my progress as well as what I learn about Copyright, Free Access, etc. |
| Computer Science Day and yet another talk… [Mailund on the Internet] Posted: 18 Jun 2008 02:08 AM CDT The coming Friday we have our annual Computer Science Day at Aarhus University. This is essentially the same as the Biology Day a few weeks back where I also gave a talk, but now at the Dept. of Computer Science, of course. The point of these days is to present our groups and our work to the other groups in the department (and to students and anyone interested in general). So it is a short presentation of the group followed by a presentation of one or two of our recent projects. Working in Bioinformatics, I guess both biology and computer science considers it part of their research, although really BiRC is a separate research center. Just with people from both backgrounds (and others). I am going to talk about the usual association mapping stuff I always talk about these days. I’ve put a lot of pictures in my slides, so it is a large download, but you can get it as PDF, PowerPoint or Keynote if you want to download the presentation. A Falsh version is here: |
| Your SNPs are your information [business|bytes|genes|molecules] Posted: 18 Jun 2008 01:50 AM CDT A quick follow up to my previous post. Reading Rob Carlson’s wonderfully written post on the C&Ds sent out by the California Department of Public Health to 13 consumer genetics companies got me thinking. He writes
That about sums it up doesn’t it. To a degree it reminded me about all the debates about intellectual property and ownership that led to the formation of Creative Commons. Biology is an information driven science and our genetic makeup is a fundamental piece of information. The WebMDs of the world provide information. Wikipedia provides information. Out of curiosity, I decided to take WebMD for a drive and look at 23andme as well (anyone can sign up for an account and explore the site). I chose a disease for which 23andme says the research is well established, Colorectal Cancer. The information includes a writeup on the biology of the disease with links out to resources like the American Cancer Society, etc. There is a hypothetical summary report as well (for the dummy family you are assigned) based on the known SNP for Colorectal Cancer. Here is what it says
One could argue that in the absence of a recognized test, this information doesn’t mean much. But note that part about information. That’s the key. This doesn’t say, you need to get yourself tested. All it tells you is about the biology of the disease and what we know about the SNP. The other key is the blurb right on top of the Resources tab
The WebMD information is rather extensive, although not half as well presented. You can do a lot of digging, and find out about when and why you might need a genetic test. I see the two services as complimentary at some point in the future, since WebMD has a much larger scope. But in the end both are information resources, to be used by us (consumers) as per our needs, interests and opportunity. To an extent, I just took a somewhat long detour. The point remains the one that Rob makes about information, and who gets to decide. In a market driven system, assuming CLIA labs are being used (there I agree with the health department), and where you are not being promised what is not possible, then, let the market decide whether these companies should exist or not. I will end with another snippet from the blog post that started this post.
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| Reductionism and Biology [Bitesize Bio] Posted: 18 Jun 2008 12:01 AM CDT The Stanford Encyclopedia of Philosophy has a great article that I found recently on Reductionism in Biology. Synthesis, or holism, is nice and all, but you can’t really understand something without identifying and understanding its constituent parts. The intro below the fold…
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| Posted: 17 Jun 2008 10:11 PM CDT Reporting in this week’s PLoS ONE, an Italian research team, consisting of Andrea Camperio Ciani and Giovanni Zanzotto at the University of Padova and Paolo Cermelli at the University of Torino, found that the evolutionary origin and maintenance of male homosexuality in human populations could be explained by a model based around the idea of sexually antagonistic selection, in which genetic factors spread in the population by giving a reproductive advantage to one sex while disadvantaging the other. Male homosexuality is thought to be influenced by psycho-social factors, as well as having a genetic component. This is suggested by the high concordance of sexual orientation in identical twins and the fact that homosexuality is more common in males belonging to the maternal line of male homosexuals. These effects have not been shown for female homosexuality, indicating that these two phenomena may have very different origins and dynamics. Male homosexuality is difficult to explain under Darwinian evolutionary models, because carriers of genes predisposing towards male homosexuality would be likely to reproduce less than average, suggesting that alleles influencing homosexuality should progressively disappear from a population. This changed when previous work by Camperio Ciani and collaborators, published in 2004, showed that females in the maternal line of male homosexuals were more fertile than average. Challenged by all these empirical data, the authors of the new study published in PLoS ONE considered a range of different hypotheses for the genetic diffusion of male homosexuality. These included: the genetic maternal effects on sons, the heterozygote advantage (as is found in malaria resistance), and “sexually antagonistic selection.” The latter is a particular aspect of Darwinian evolution, in which genetic factors spread in the population by giving a reproductive advantage to one sex while disadvantaging the other. This type of evolution has been previously found in insects, birds, and some mammals, but never in humans. To discover and clarify the dynamics of the genetic factors for homosexuality, the researchers had to screen a large set of models and exclude them one by one. They concluded that the only possible model was that of sexually antagonistic selection. The other models did not fit the empirical data, either implying that the alleles would become extinct too easily or invade the population, or failing to describe the distribution patterns of male homosexuality and female fecundity observed in the families of homosexuals. Only the model of sexually antagonistic selection involving at least two genes – at least one of which must be on the X chromosome (inherited in males only through their mother) – accounted for all the known data. The results of this model show the interaction of male homosexuality with increased female fecundity within human populations, in a complex dynamic, resulting in the maintenance of male homosexuality at stable and relatively low frequencies, and highlighting the effects of heredity through the maternal line. These findings provide new insights into male homosexuality in humans. In particular, they promote a focus shift in which homosexuality should not be viewed as a detrimental trait (due to the reduced male fecundity it entails), but, rather, should be considered within the wider evolutionary framework of a characteristic with gender-specific benefits, and which promotes female fecundity. This may well be the evolutionary origin of this genetic trait in human beings. The possible widespread occurrence of sexually antagonistic characteristics in evolutionary processes, which play their evolutionary game by giving a fecundity benefit to one sex while disadvantaging the other, has only recently begun to be appreciated. This is understood as a key mechanism through which high levels of genetic variation are maintained in biological populations. Male homosexuality is just the first example of an unknown number of sexually antagonistic traits, which contribute to the maintenance of the natural genetic variability of humans. The new perspectives opened by the models developed for sexually antagonistic selection may also contribute to a better understanding of most genetically-based sexual conflicts, which are, at present, poorly understood in humans. An unexpected implication of the new models concerns the impact that the sexually antagonistic genetic factors for male homosexuality have on the overall fecundity of a population. The findings suggest that the proportion of male homosexuals may signal a corresponding proportion of females with higher fecundity. Consequently, these factors always contribute, all else being equal, a positive net increase of the fecundity of the whole population, when compared to populations in which such factors are lower or absent. This increase grows as the population baseline fecundity decreases; this means that the genes influencing male homosexuality end up playing the role of a buffer effect on any external factors lowering the overall fecundity of the whole population. Source: Public Library of Science Josh says: Wow. While they did not actually find a gene mutation linked to this, the data fits the model. Certainly it provides an explanation, and I personally like it better than many other explanations. However, whether a male is homosexual or heterosexual cannot be solely genetic, but rather is more likely a genetic predisposition (though I could be wrong). So what about this type of mutation would create such a predisposition? Note: For those not familiar with the term, fecundity refers to how fertile a female is or how many offspring are produced. |
| Modeling Mating and Information Processing in A Yeast Cell [adaptivecomplexity's column] Posted: 17 Jun 2008 09:54 PM CDT One of the major challenges in molecular biology right now is to understand how different parts work together to produce the behavior of a cell. A cell can't really be explained by the biological equivalent of an organization chart - you can't say, "this protein does this, this other one over here does this, that one has this job..." That works for some functions, but many of the processes in a cell come about because of the way regulatory links are organized into feedback loops. This means that, when we look at the complex wiring of a cell's information processing machinery, our intuition will only take us so far. To really understand how things work, we need to make mathematical models, and we need to make careful biochemical measurements to test those models. This is the way to really understand how the whole of the cell is greater than its parts. Writing in Molecular Cell, a group at the University of North Carolina has looked into the behavior of a protein called Fus3. Fus3 is at the bottom of a chain of signal-passing events that tell yeast cells that there is a potential mating partner around. |
| R'Uh-R'Oh Shaggy!!! [The Gene Sherpa: Personalized Medicine and You] Posted: 17 Jun 2008 09:25 PM CDT You know. I have been racking my brain why all of these "early adopters" kicking me on this blog have such an aversion to going to see a doctor. They claim that they want information, but I ask "How... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| A$$ Kicking [The Gene Sherpa: Personalized Medicine and You] Posted: 17 Jun 2008 07:09 PM CDT Whoah! I never thought that my blog would generate such response! I received over 100 emails today. Guess what. In a near 50/50 split they were pro or anti regulation. Some were so nasty and hate... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
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