Wednesday, February 28, 2007

Which Came First, The Lactase or the Cow?

How's this for a random evolution-related debate:

"Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in central and northern Europeans in the last 20,000 years. This trait is likely to have conferred a selective advantage in individuals who consume appreciable amounts of unfermented milk. Some have argued for the "culture-historical hypothesis," whereby LP alleles were rare until the advent of dairying early in the Neolithic but then rose rapidly in frequency under natural selection. Others favor the "reverse cause hypothesis," whereby dairying was adopted in populations with preadaptive high LP allele frequencies."

Weighing in on this debate, the authors of the above excerpt sequenced the lactase locus in the DNA samples of 9 different 7,500 year-old human skeletons from Eastern Europe. Although the skeletons date to well after the domestication of cattle, their latest results, just published in PNAS, show that these individuals did not possess the lactose tolerance allele. These findings therefore lend support to the hypothesis that the domestication of cattle was a driving force behind the evolution of lactose tolerance in human adults. Sadly, we still know very little about what drove the evolution of chocolate milk-producing cows.


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Monday, February 26, 2007

Drug company funding guarantees positive results

This one hits close to home. But before starting to question the integrity of scientists it's good to remember that companies are risk averse and probably back up safer studies: "Breast cancer studies funded by drug companies are more likely to yield positive findings than those without pharmaceutical industry backing, according to research published on Monday."


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Top 200 universities

Stolen from Digg comments. Guess which one didn't make the cut...

1 Harvard University United States
2 University of Cambridge United Kingdom
3 University of Oxford United Kingdom
4= Massachusetts Institute of Technology United States
4= Yale University United States
6 Stanford University United States
7 California Institute of Technology United States
8 University of California, Berkeley United States
9 Imperial College London United Kingdom
10 Princeton University United States
...
21 McGill University Canada
27 University of Toronto Canada
50= University of British Colombia Canada
133= University of Alberta Canada
155 McMaster University Canada
176 Queen's University Canada
181= University of Montreal Canada

By country:
55 in the US,
29 in the UK,
14 in Australia,
11 in Japan,
11 in Netherland,
10 in Germany,
7 in France,
7 in Canada,

by population density:
1 per 1.07m in Switzerland
1 per 1.48m in Australia
1 per 1.49m in Holland
1 per 1.49m in Singapore
1 per 1.76m in HongKong
1 per 1.81m in Denmark
1 per 2.08m in Belgium
1 per 2.09m in UK
1 per 2.28m in Sweden
1 per 2.37m in Israel
1 per 2.76m in Austria
1 per 4.69m in Canada


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A Juicy Steak Melts more Glaciers than Your Car

Ok I'm not a vegan and I like my steak as much as anyone, but the shocking results of this United Nations study on the environmental impact of global livestock production are making me think twice (read the actual report here). Global warming is garnering quite a bit of media attention these days (ie Al Gore got his oscar last night for "An Inconvenient Truth"), but nobody's talking about these sobering facts:

  • The livestock sector contributes 18% of human-related greenhouse gas emissions, a larger share than even the transport sector. This is mostly due to the production of massive quantities of methane and nitrous oxide, which each have 23 and 296 times greater warming effects than carbon dioxide.
  • Livestock use 30% of the Earth's terrestrial land surface, including 70% of the Amazonian rainforests that have been clear-cutted to date.
  • Livestock production takes up 70% of all land currently dedicated to argiculture (including pastures and feed crops).
  • 8% of human water usage is dedicated to the irrigation of livestock feed crops.
So while it's obviously important that we reduce fossil fuel combustion by driving less and developing alternative energy sources, this report just highlights the fact that by far the greatest challenge to human survival is feeding ourselves in a sustainable, less resource intensive way. If we continue to practice agriculture as we do currently, it will kill us.


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Sunday, February 25, 2007

Mapping the Cancer Genome

Get a glimpse of the future of genetics in a nice Scientific American article by Francis S. Collins and Anna D. Barker. Here's an excerpt:

"If we wish to learn more about cancer, we must now concentrate on the cellular genome." Nobel laureate Renato Dulbecco penned those words more than 20 years ago in one of the earliest public calls for what would become the Human Genome Project. "We are at a turning point," Dulbecco, a pioneering cancer researcher, declared in 1986 in the journal Science. Discoveries in preceding years had made clear that much of the deranged behavior of cancer cells stemmed from damage to their genes and alterations in their functioning. "We have two options," he wrote. "Either try to discover the genes important in malignancy by a piecemeal approach, or & sequence the whole genome."

Dulbecco and others in the scientific community grasped that sequencing the human genome, though a monumental achievement itself, would mark just the first step of the quest to fully understand the biology of cancer. With the complete sequence of nucleotide bases in normal human DNA in hand, scientists would then need to classify the wide array of human genes according to their function--which in turn could reveal their roles in cancer. Over the span of two decades Dulbecco's vision has moved from pipe dream to reality. Less than three years after the Human Genome Project's completion, the National Institutes of Health has officially launched the pilot stage of an effort to create a comprehensive catalogue of the genomic changes involved in cancer: The Cancer Genome Atlas (TCGA).


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The smell of food can kill you

We have previously discussed the subject of caloric restriction and longevity to great lengths. However, in a surprising twist, it seems that just the smell of food can reverse the anti-aging benefits of dieting: "Smell is an ancient sensory system present in organisms from bacteria to humans. In the nematode Caeonorhabditis elegans, gustatory and olfactory neurons regulate aging and longevity. Using the fruit fly, Drosophila melanogaster, we showed that exposure to nutrient-derived odorants can modulate life span and partially reverse the longevity-extending effects of dietary restriction. Furthermore, mutation of odorant receptor Or83b resulted in severe olfactory defects, altered adult metabolism, enhanced stress resistance, and extended life span. Our findings indicate that olfaction affects adult physiology and aging in Drosophila, possibly through the perceived availability of nutritional resources, and that olfactory regulation of life span is evolutionarily conserved."


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Can tests predict you ability to succeed in graduate school?


This meta-analysis suggests so. However the correlation with citation seems low. what do you think? "Research has been conducted on the correlation between test scores and various measures of student success: first-year grade point average (GPA), graduate GPA, degree attainment, qualifying or comprehensive examination scores, research productivity, research citation counts, licensing examination performance, and faculty evaluations of students. These results are based on analyses of 3 to 1231 studies across 244 to 259,640 students."


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Attack of the Killer Frogs


Rana Catesbeiana, the American Bullfrog, is a voracious predator (believe it or not!) that will eat just about anything that it can fit in its mouth. These frogs are native to eastern North America. In the 1930s, the bullfrog was introduced to British Columbia to cultivate for their tasty legs. Since then, the frog has spread on Vancouver Island and reached mainland BC, outcompeting and displacing native frog populations and becoming an environmental concern. This is similar to other foreign species introductions, most notably the giant toad and european rabbit introductions in Australia. For a list of other detrimental species introductions, check this link out and be careful what you import!


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Thursday, February 22, 2007

Gene Patents

Coward's recent post about prestin got me thinking about gene patents and how they work. While I couldn't find a decent overview of Canadian guidelines at the Canadian Intellectual Property Office, I did come across 2 other good resources. The first is a summary of British gene patent information and the other is an excellent FAQ from the Human Genome Project. The rules are pretty similar. Basically, to patent a gene:

1) it must be a novel sequence
2) you must specify the gene product
3) you must specify the product function

The last two points are key, as they prevent the massive patenting of sequences and sitting on the rights until somebody else comes up with a practical application (see: submarine patents).

Interestingly, ESTs and SNPs can also be patented which means there is the potential for multiple patents on the same sequence. Whole organisms can also be patented, provided they are not naturally occurring (GM corn, for example), as can naturally occurring substances, as long as a novel use can be specified.

Currently an estimated 20% of human genes have been patented, but fortunately the government reserves the right to override patents in cases where it is deemed vital for the public good and the patent holder is being overly restrictive. For example, the American Medical Association has asked for a ban on patents for medical and surgical procedures, or, closer to home, the Ontario government ignored a US patent on a cancer screen and offered the test to the public. Similarly, the BC government complied and stopped, but has since resumed offering the test.


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New source of income for grad students

Grad students will do just about anything for extra cash/food. Sell blood, semen or spend 6h motionless looking at med students writing exams. Now you might even be able to sell your eggs for stem cell research at 500$ a pop, at least if you live in the UK. Doesn't seem like much of a deal to me, since apparently, if you're an Ivy Leaguer with a high IQ you can sell your sperm or eggs for reproductive purposes at close to 40 000$ a load. Scroll to see all the comments from woman who want to sell eggs : "I have a 147 I.Q., 3.9 GPA, Brown hair, brown eyes, 5'4 115 pounds, and I also am a very skilled artist."


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Tuesday, February 20, 2007

IA updates


Once again I order you all to check out http://www.informationaddiction.com, where the links flow like that guys ear hair in the last post.
Some good stuff on the usual net neutrality debate, Zoom Player has a new version (love zoom player), and another Paris Hilton video (I haven't checked it out but hopefully NSFW).


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Shape-shifting molecular motor in your ear

Prestin is a membrane protein found in the hair cells of the mammalian cochlea and a member of the anion transporter familly. It is essential for hearing in mice, and KOs have a 40-60dB (>100 fold) loss in hearing sensitivity. It is essentially a direct voltage to displacement motor, that does not use ATP and is the fastest molecular motor identified by several orders of magnitude. In response to the change in voltage (Cl and bicarbonate) the Prestin changes the shape of the cell and the stiffness of the hair. When overexpressed in kidney cells, it could still work in the same way and induce shape-shifting. Interestingly it can also work in the other way around and transform movement into voltage, making a molecular generator. Of course the DNA sequence was rapidly patented in 2003, and now NASA is taking interest in it and wants to make bugs that can make energy to insert into astronaut's space suits and power them by their movement. Sounds far out, but really I can't wait until we start building nano-robots with it...


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Don Cherry lobbies for natural product in Canada


Apparently Cold-FX works according to Health Canada. Clinical trials do exist that strongly suggest that Cold-FX, a ginseng derived therapy, prevents and cures colds and flu. Health Canada has given it a natural product number and therefore has approved it's claims as stated on the bottle. CV-technologies, the company that pimps Cold-FX, had a massive stock price jump upon the news of the approval. Don Cherry, once up for 'best Canadian of all time' or something like that, pimps for Cold-FX (and Quiznos) and according to this article I just read perhaps physically intimidated Stephen Harper (link to info on his podcast) into issuing the natural product number to Cold-FX and CV-technologies. Awesome.
CV-technologies also has Remember-FX, which apparently also has passed muster on a clinical trial, although I can't find it.


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Video Games Make You a Good Surgeon

Ok, so now studying for a med school exam is just no longer a valid reason for not coming to LAN parties. Apparently, playing video games makes you a better surgeon. No word on which games are the best practice for surgery, but I'm guessing Call of Duty and anything on the Wii are right up there. I'm sure they'll have Wii surgery eventually, although I don't see them ever being as much fun as those crazy Japanese games.


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Thirty Years of Stem Cell Randomness (As Discussed on the Bayblab Pubcast)

As discussed previously on the bayblab podcast (Episode 6 part 3) it was Canadian research pioneers Till, McCulloch, and Siminovitch who first discovered hematopoietic stem cells and, amongst other things, described their perplexing stochastic behaviour. Through elegant experiments involving serial passage of bone marrow derived "spleen colony-forming" HSCs in live mice (they didn't have the funding to use the high-tech and expensive system known as "cell culture"), they nicely demonstrated that the fate of individual daughter cells resulting from stem cell mitosis is not predictable or deterministic, but rather stem cell division is a probabilistic event when large populations are observed. A short paper, well-written and definitely worth the read (A STOCHASTIC MODEL OF STEM CELL PROLIFERATION, BASED ON THE GROWTH OF SPLEEN COLONY-FORMING CELLS. PNAS, 1964). I also posted the figures below just because they're so 60s cool. I don't know exactly what people in the field thought at the time the paper was published, but my interpretation is that biology hasn't really been equipped to explain this type of behaviour, until just recently technical advances have allowed us to look at gene expression and other cell behaviours in real time at the single-cell level.

Thirty years later, these types of approaches are reveleaing the fascinating dynamics of cell behaviour. Case in point: today's lecture at the OHRI by Eric Jervis, an engineer from the University of Waterloo, who has built custom technology to microscopically observe and track the behaviour of large numbers of individual cultured cells. The cells are captured on digital video and lingeages tracked over multiple rounds of cell division. Lineages were visualized on a typical pedigree type diagram. Anyway, the videos were just too awesome to convey in words. Not many of them can be found in published literature, but this cool one from a 2006 PNAS publication (click on the image below to view the video) captures individual hematopoietic stem cells in the act, giving rise to colonies of highly variable cell number and proliferative rates upon explant into culture. Strikingly similar findings to those of McCulloch, Till and Siminovitch thirty years ago, now live and in digital format...


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Monday, February 19, 2007

Tongue-tied: The evolution of speech

This comes from an old conversation that I was reminded of recently. Compared to the rest of the animal kingdom, humans fall short physically in a number of ways. Eyesight isn't as great as some, hearing and sense of smell worse than others. I could go on. Yet humans have dominated the face of the planet, and this is in no small part because of language. Sure, the ultimate reason is intelligence, which means we don't need to rely as strongly on pure physical assets. But what good are plans and ideas if they can't be communicated. An evolution beyond primal vocalization (grunts, growls, etc.) has allowed for the sharing of ideas, coordination of effort through communication and dissemination of knowledge and information. But when did the skill of speech being to arise?

In the 1970s, using human and chimpanzee models, the larynx of a neanderthal fossil was reconstructed leading the researchers involved in the study to conclude that neanderthal was incapable of human speech. This reconstruction was disputed based on the placement of they hyoid bone (which was unlike the position in newborn or adult humans, stillborn chimpanzees or adult chimpanzees and positioned on the basis of ability to swallow) and whether neanderthal man could speak remained uncertain.

In 1989, new neanderthal fossil evidence - a well preserved hyoid bone identical in size and shape to modern humans - indicated that indeed at least the skeletal structures and morphology necessary for speech were present at this stage in human evolution, and has changed little in the past 60 000 years. Of course, this alone doesn't prove that Neanderthal man was capable of speech, but along with other evidence - adequate brain development, and social organization that would necessitate some form of higher communication - certainly suggests that this was the case.

More recent computer simulations based on models of neanderthal vocal tracts demonstrated that if the larynx was posistioned like that of humans, the voice would have been extremely low and difficult to communicate effectively with. If it was positioned like that of a chimp, the words would be "slushy and difficult to understand."

The problem with any model of the vocal tract is that the ability to speak is dependent on the larynx, tongue and other soft tissues that don't fossilize well so their size and position in neanderthal man is speculative at best, but with evidence both for and against neanderthal speech a consensus in this debate is unlikely to be settled soon.

On the other hand, there may be a genetic answer to the neanderthal speech question: FoxP2. This highly conserved gene is required for some of the developments necessary for speech and tracing it's evolution could give answers as to when language developed.


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Bayblab Podcast Episode 6 Part 3 - The Elusive Stem Cell

On this installment of Bayblab Podcast Episode Six (The Pubcast), Rob ridicules my blasphemous assertion that stem cells do not exist, setting the stage for a raucous barroom brawl as we fight to the death in a tag-team contest for intellectual supremacy. Also Kamel discusses his massive testicles, Coward outlines his approach to experimental research and we discuss why none of us will ever make an important contribution to science.


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Friday, February 16, 2007

Antisense and evolution

Since I'm digging up old Kenster stories I thought I should mention this one...While the switch from the RNA world to the DNA->RNA->protein world remains a mystery there is no shortage of opinion on how that transition might have happened. One of such theories states that there is actually a structural link between RNA sequence and protein sequence. So for example if you were to take the receptor RNA and take the antisense strand of that receptor, it would generate a peptide that would be sticky to the receptor, however it has long been debunked: "We followed an approach which predicts that translation of two complementary RNA strands into protein generates pairs of "antisense" peptides which bind each other with specific and high affinity (Bost et al. Proc. Natl. Acad. Sci. (1985) 82, 1372). We used human parathormone as an experimental example, and we analysed by computer homologies between antisense peptide sequences and their published receptor sequences. We conclude that there is no experimental indication that parathormone binds to a synthetic peptide, the sequence of which was derived from the antisense RNA sequence. Based on homology scores and antigenicity indexes (Hopp) the analysis shows that the peptide ligand itself, or a random artificial peptide, are as good candidates as the antisense peptide in producing antibodies, presumably recognizing the receptor. We therefore question the general applicability of this approach"

Some people also beleive that the antisense strand has the capacity of encoding functional peptides and may be important during evolution for the formation of new genes when there is an inversion: "The question whether the noncoding DNA strand had or still has the capability for encoding functional polypeptides has been addressed in several articles. The theoretical background of the views advocating this idea arose from two groups of findings. One of them was based on various observations implying that the genetic code was adapted for double-strand coding. The other group of theories arose from the observation of gene-length overlapping open reading frames (O-ORFs) on the antisense DNA strand in a number of genes. In fact, the above theories, which I term selectionist, conceive a novel conception of gene evolution, proposing that new genes can be created by the utilization of antisense DNA strand. In contrast, neutralist theory claims that the O-ORFs are mere by-products of evolutionary processes acting to create special codon usage and base distribution patterns in the coding sequences"


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Shooting pigs with automatic riffles

In a story that would make PETA people cry, pigs are routinely used for trauma training. Another Ken-meister gem: "The idea is to work with live tissue. You get a pig and you keep it alive. And every time I did something to help him, they would wound him again. So you see what shock does, and what happens when more wounds are received by a wounded creature. My pig? They shot him twice in the face with a 9-millimeter pistol, and then six times with an AK-47 and then twice with a 12-gauge shotgun. And then he was set on fire. I kept him alive for 15 hours. That was my pig."


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Sharks DO get cancer

I just gave a journal club about a trio of papers out this week in Nature Genetics. They support an interesting theory that stem cell and cancer cell self renewal is controlled by Polycomb repressor complexes (PcG). They maintain tumour supressors in a repressed but still free to be activated and thus "bivalant" chromatin environment in stem cells. However with time and because of epigenetic drift these supressor complexes tend to recruit DNA methylation and the tumour supressor become irreversibly repressed, thus with a "locked-in" stem-ness. This could be regarded as the "first" hit of the two hit transformation driving a stem cell into a cancer cell. Interresting paper, although you never know these days whether to trust stem cell papers, I guess the gold rush mentality attracts fraud.
Following JC I discussed the significance of said papers with the Ken-meister, and proposed that maybe sharks do not keep stem cells around and that is why they don't develop cancer. To which Ken replied yes they do! So I must correct myself from the podcast, although the incidence rate is low compared to other fish there has been cases of tumours including Chondromas! Oh the irony, I guess shark cartilage is not going to save you, however wrestling shark while intoxicated on vodka is still ok...


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Aubrey De Gray is still alive

Aubrey keeps on coming up on my internet searches and he, annoyingly, must be getting money. Check out the SENS (strategies for engineered negligable senescence) website where they link to their scientific journal that is included in the pubmed database, Rejuvenation Research. EMBO published a revealing debate in 2005 both pro-Aubrey and anti-Aubrey. The anti-Aubrey article sums up my feelings on the debate quite well whereas the article by Aubrey de Gray speaks mostly about why there is resistance to his ideas on a political level, not much on a scientific level. Good stuff.


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Thursday, February 15, 2007

Squid are Badder-Asser Than You Think

Of course on dry land squid might be nothing more than an amorphous blob of jelly (or an ink-squirting toy for Newfies), but if you run into one in the deep sea you might be in trouble. Check out the video footage of this bad-ass squid on the prowl as it shows off its bioluminscence. Freaking cool. Also check out the giant squid attacking this diver (sadly no bioluminscence).


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Wednesday, February 14, 2007

The science of love


There are a few stories out there that caught my attention. The first one involves the size of the tail in male fish: "female green swordtail fish mature more rapidly if they spot a male with a big tail. Likewise young males retard their sexual development for several months if they spot a better-endowed male". You're free to make your own conclusions on that one. The second story shows a link between vasectomy and dementia, I bet you didn't see that one coming. Finally a third story shows that nagging does not work since even when shown the name of the significant other subliminally, you are less likely to perform a task. From the article "The main finding of this research is that people with a tendency toward reactance may nonconsciously and quite unintentionally act in a counterproductive manner simply because they are trying to resist someone else's encroachment on their freedom.".
But My favorite is this article on which region of the brain is reponsible for the feeling of love itself. I love it when scientists talk dirty like that: "Dr. Brown said scientists believe that when you fall in love, the ventral tegmental floods the caudate with dopamine. The caudate then sends signals for more dopamine. The more dopamine you get, the more of a high you feel [...] Lots of dopamine, in turn, triggers the production of testosterone, which is responsible for the sex drive in both men and women." . One of the experiments in question that made people cry in an MRI machine reminds me of Dr. House :"Now their research is centered on the flip side of love. They've recruited college students who'd just been rejected by their sweethearts. Again, the scientists performed MRI's while these students looked at photos of the objects of their affection."


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Monday, February 12, 2007

Vitamin D, Sunlight, Folate and Race

Another lunch time discussion turned bayblab post.
Apparently skin colour evolution is linked to folate and vitamin D. The most amusing part of this excellent article is that people with dark skin in higher latitudes can develop rickets if they don't get enough sun. I didn't know that people actually got that disease anymore since the fortification of milk. I also thought that vitamin D deficiencies were related to seasonal affective disorder (SAD), but I haven't found anything about darker skinned individuals being more prone to this disorder. In fact they seem to be just as prone as the general population. strange.
Related to the podcast discussion (part III of episode 6 yet to come out) on continuing human evolution I wonder if there is any selective pressures on skin colour due to vitamin D and/or folate in any parts in the world today.


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Darwin was forgetful

Darwin was heavily criticized for not acknowledging some of the work he drew inspiration from that preceded Origin of Species. He was even accused of plagiarism. Well it turns out that he simply forgot to include the preface of his book when he sent it to the publisher.

As a side note, He also forgot to adequately explain the evolution of permanent large breast in humans by sexual selection. I always thought it was selected by man as a predictor of good maternal lactation, but the story is a lot more interesting : "Another false “bigger is better” argument is that which says that a man will find big breasts sexy because he knows that any children he fathers by the breasts’ owner will not go hungry. In fact, the breasts on a nullipara contain mainly fat, not milk-producing tissue. They are almost no indication at all of the amount of milk a woman might produce in the future. Breasts typically increase in size for the first eight months of lactation. Besides, an ability to produce more milk than is needed is no advantage. Once a woman has produced enough to feed her baby well, any excess production is expensive waste. Almost all women can produce enough to feed a child. Milk production increases to meet demand, so a woman bearing twins will produce more (2)."

On a related topic (and author)" check out this guy's explanation of the evolution of fat thighs: "There was a definite cost of a paunch. Paunches are not sexy. The reason a paunch on a woman is not sexy is simple. A woman with a paunch looks pregnant, and pregnant women are in no state to be impregnated by a man, and so men’s instincts will evolve to find big prominent bellies unsexy. In order to avoid appearing pregnant, women evolved to deposit fat stores away from the belly, and the next nearest place was the backside and thighs. Here, the cost of encumbrance was that women could not run quite as fast as otherwise they might, but the benefit of looking more fertile was greater than that cost."


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Thursday, February 08, 2007

Bayblab crew dominates

Hard to imagine these same guys could inflict so much trivia damage .


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Collagen flavoured lunch

Just to settle a lunch time discussion about gelatin.
I was TAing a lab where some of the homogenized chicken breast muscle was coagulating. Some of the technicians thought that it correlated with the length of time that the muscle was homogenized. However it might be that different groups had different amounts of connective tissue in their chicken breast and therefore they had some collagen polymerizing into gelatin.
All you need to know about gelatin is in the wikipedia entry.


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Species named after celebrities

Just for laughs you can check out this site which has 9 examples of species named after celebrities. They have some good ones such as a rabbit named after Hugh Hefner, slime mold beetles named after members of the Bush administration, and flies named after Bill Gates and Paul Allen. There is even a blind cave bug named after Hitler that is facing extinction because of collectors. In fact there is a long history of bugs being named after people to insult them. The most famous story is in the "19th century, when entomologists Mr. Chase and Mr. Dyar were engaged in a collecting war. When Mr. Chase found a liparid moth, he named it "in honour" of his rival: The moth is now known as Dyaria, and a target of scatological fetishists everywhere.". Not to mention all the rock bands: "A team of palaeontologists with poor music tastes named a Madagascan dinosaur masiakasaurus knopfleri, after Dire Straits singer Mark Knopfler. There is Bufonaria borisbeckeri (a marine snail), Hyla stingi (a Colombian tree frog) and a wasp called Polemistus Chewbacca. In 1994, a fossil chaoborid fly was named "I", until a researcher pointed out that he didn't want to keep writing "I have small male genitalia." (it was changed to Iyaiyai). There's even another hitleri - a paleodictyoptera (flying insect fossil) named in 1934."


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Wednesday, February 07, 2007

The Quotable Sidney Altman Talks at U of O

Nobel prize winner (for discovering the ribozyme activity of RNAse P) Sidney Altman visited from Yale to give a talk at the U of O today on RNA-based therapeutics. The talk started with a tantalizing glimpse of the man's brilliance as he outlined the many unanswered questions regarding the origins of life on Earth. However this brief introduction came to an abrupt end when he declared that neither he nor anyone else currently has any answers to offer, and then proceeded to give a fairly uninspired talk on the therapeutic potential of sequence-specific RNAse P mediated gene knockdown (although now that I write it out it is kind of cool). In spite of this, the question period made attendance well worthwhile, where Altman held no punches.

The best quote came when he was asked if he cared to speculate on how protein-based life evolved in the RNA world. His answer (I paraphrase): "No. No I wouldn't care to speculate. Not because I'm trying to be rude, but because I don't have any good ideas. I have lots of ideas, but they're bad ideas, and there's no point in discussing my bad ideas with you. Actually I don't think anyone has any good ideas yet, and there are a lot of people that are spending most of their time thinking about this problem, whereas I only think about it while I'm in the bathtub. So I certainly have no good ideas."


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Meet the World's Greenest CEO

Thought I'd mention an interesting interview I randomly caught on The Hour with the so-called "World's Greenest CEO", Ray Anderson. Founder of carpet manufacturer Interface, Inc., this guy is genuinely interested in creating sustainable, even restorative industry, and as a proven money-maker, has the skills to convince people that it can be economically viable. Apparently his factories have already virtually eliminated solid waste and carbon monoxide emissions, and are now focused on moving toward petroleum-free products and total sustainability. Anyway, I can't really summarize without it all sounding like boring rhetoric, so check out this interview and you'll see what I mean.

He also mentions a book by Paul Hawken, The Ecology of Commerce, as his inspiration. Sounds interesting.

Anyway nice to see that capitalists out there also care about the future of life on Earth...guess they're people too.


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Burgess Shale & Hox genes


I was looking for stuff to post about the Burgess Shale because it's cool and Bayman at one point was going on about the Cambrian explosion being problematic. The burgess shale is a site in British Columbia containing many fossils from this evolutionary explosion of diversity.
However I found another blog entry at The Voltage Gate that basically kicks ass on how much effort I was going to put in. Check out this awesome blog entry on the Burgess Shale at The Voltage Gate. I was hoping to be able to find some more information on how the explosion might relate to the evolution of Hox genes, that is the genes that are largely responsible for body plan, but I was not very successful. Luckily first hit on Google I got was a link to an Intelligent Design quiz on the Cambrian explosion. I did find a couple of reviews that summerize research into Hox gene evolution that indicate Hox gene diversity predated the Cambrian explosion. I totally don't get it.


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Tuesday, February 06, 2007

Protein synthesis: an epic on the cellular level


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Monday, February 05, 2007

The Evolution of Life: Not What Your Momma Taught You

In biology I think we all pretty much take for granted the fact that all life on Earth is the evolutionary product of three distinct cell type lineages, the Bacteria, the Archaea, and the Eucarya, which were themselves the descendants of a common cellular ancestor (whose exact nature is now lost to us). This concept derives primarily from the so-called "universal phylogenetic tree" assembled based on a comparison of ribosomal RNA sequences of various types of cells. Indeed, the rRNA tree was one of the great accomplishments of the molecular era of biology, seeming to represent irrefutable evidence supporting Darwin's theories of common descent formulated a century or so earlier.

However, Carl Woese, who first came up with the universal rRNA phylogeny (also defined the Archaea as a new kingdom and originated the RNA world hypothesis), points out that the origin of life is not so clear cut. Although the rRNA tree gives a nice phylogeny that is agreeable with classical taxonomy, you run into problems when you start to try to compare trees based of sequences of different genes and proteins. For example, the Archaea and Eucarya might have the highest degree of homology when you compare gene A, but the Archaea might be more homologous to the Bacteria with respect to gene B. Apparently the frequency of these conflicts becomes more and more of an issue the further back you go through the tree, to the point where talking about three primitive and distinct cell types and trying to make inferences about their common ancestor doesn't even make any sense. Thus, he writes extensively about the need to develop and test new theories concerning the origins of cellular life. I've been checking out a few of his more recent reviews on the topic and they're pretty provacative and fun to read. Some interesting exerpts regarding the origins of cellular life:

The Annealing Model From The Universal Ancestor:

"A genetic annealing model for the universal ancestor of all extant life is presented; the name of the model derives from its resemblance to physical annealing. The scenario pictured starts when "genetic temperatures" were very high, cellular entities (progenotes) were very simple, and information processing systems were inaccurate. Initially, both mutation rate and lateral gene transfer levels were elevated. The latter was pandemic and pervasive to the extent that it, not vertical inheritance, defined the evolutionary dynamic. As increasingly complex and precise biological structures and processes evolved, both the mutation rate and the scope and level of lateral gene transfer, i.e., evolutionary temperature, dropped, and the evolutionary dynamic gradually became that characteristic of modern cells. The various subsystems of the cell "crystallized," i.e., became refractory to lateral gene transfer, at different stages of "cooling," with the translation apparatus probably crystallizing first. Organismal lineages, and so organisms as we know them, did not exist at these early stages. The universal phylogenetic tree, therefore, is not an organismal tree at its base but gradually becomes one as its peripheral branchings emerge. The universal ancestor is not a discrete entity. It is, rather, a diverse community of cells that survives and evolves as a biological unit. This communal ancestor has a physical history but not a genealogical one. Over time, this ancestor refined into a smaller number of increasingly complex cell types with the ancestors of the three primary groupings of organisms arising as a result."

The Role of Horizontal Gene Transfer (from On The Evolution of Cells):

"A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the "Darwinian Threshold" for the reasons given."

Other Carl Woese papers worth checking out:





6 comments:

Only YOU can prevent triple shotgun murders


Everybody knows the lifeblood of a graduate student is caffeine, but it's a delicate art maintaining a fine balance between productive caffeine levels and unproductive frequent bathroom breaks resulting from over consumption of coffee and Coca-cola. Now it's possible to get that buzz and the associated benefits without having to fight off PIs for the last drips from the pot. Get your fix in the shower, while encouraging the growth of a luxurious head of hair, with caffeinated soap. Better yet, a South Carolina scientist has figured out a way to bake caffeine into pastries without the associated bitter taste. Imagine if your morning routine was a double threat of a large double-double and a caffeine laden donut. So grab a buzzed bagel before hitting the gym to load up on carbs, keep you alert and ward off that post-workout muscle soreness.


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Sunday, February 04, 2007

Lab accident cures cancer

The story goes like this: Grad student works on GI inflammation and uses an epithelial cancer cell line as a model. Tries to see if a PPAR-Gamma modulator would be effective against Chron's disease or ulcerative colitis, but messes her calculation by a couple of logs. Result, the cells die, and she claims to have found cure for cancer. Apparently the microtubules "disapeared", but we don't know how or why. Which makes me think I have already found the cure for cancer several times over, I just didn't realise.
Top ten cures:
  1. Serum starvation
  2. Low PH
  3. Gram negative bacteria
  4. Mycoplasma
  5. Fungus
  6. Autoclave
  7. Summer student
  8. Alcohol
  9. Trypsin
  10. protein lysis buffer


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Saturday, February 03, 2007

Bayblab Pubcast

After a long hiatus, the bayblab podcast comes back with force with a new formula. The recording is live at a pub of our choice with live audience (of exactly one female) as we discuss the topics of organic food, human evolution and stem cells.
  1. As we enjoy our industrial GM'ed beer concoctions at a local pub we focus the first part of the discussion on organic foods: what does the organic label mean, is there scientific basis for claims of superior "healthyness" and does readopting ancient farming techniques really benefits mankind.
  2. In the second segment of the bayblab pubcast we discuss human evolution, modern natural selection pressure, memes and pandemics. Plus can kamel sing my little teapot?
  3. Stem cells: Do they exist, or are they just a figment of Rob's imagination?



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Thursday, February 01, 2007

The little dynein the could

My cell regulation class is in the midst of learning the intricacies of the cytoskeleton right now. To complement his lectures Jonathan Lee from the CMM department showed us this video that a student found. Some one at Harvard had alot of time and a supercomputer on their hands.

From what I've learned in the past couple of weeks its fairly accurate. The movie gives a good sense of the scales inside the cell as well as compressing about 4 years of my undergrad into 4 minutes. If you're not in the mood for some really cheesy dramatic music I suggest you turn down your speakers, if you are: turn up the bass.


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Steakilicious - name that cut


I was at a fancy steak place not too long ago. The waiter went on and on about the subtleties of the differences of the prime cuts of steak they had on the menu. I wanted to ask him about where on the cow they were from but I didn't think he would know. We are constantly getting more and more distant from where our food actually comes from. How do you do?
Check out the pic and name that cut and where on the cow it comes from.
I did poorly. Where are the obvious cuts, like cow tongue?


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Hutchinson-Gilford Progeria Syndrome


I remember seeing kids with Hutchinson-Gilford Progeria Syndrome on Maury Povich or some other lame talk show a long time ago. The afflicted individuals age prematurely and therefore provide insight into the aging process in general. PLoS has a great summary of some of the knowledge that has been gained into aging from the single gene mutation that is associated with the disease. Apparently it may all come down to accumulation and defective repair of DNA damage. The pic is of a mouse model of the disease. If you don't know already what patients with Hutchinson-Gilford Progeria Syndrome look like check out the PLoS link.


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What is she saying?

Some good captions here: "Due to a last minute substitution of featured speakers, the woman hiding in the podium was not the only one surprised."


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