Tuesday, October 29, 2013

Botfly parasite in Wired magazine

There's a nice write up of botfly larvae, which grow within the skin of humans and other mammals, at Wired magazine.  The mother fly actually uses mosquitoes as a delivery vehicle, laying her eggs on the mosquito. When the mosquito approaches a warm body, the eggs hatch and drop off onto the host, then burrow into the skin. Not for the squeamish!

Sunday, October 20, 2013

Biomarkers to detect Alzheimer's disease before the symptoms start

Alzheimer's disease is a devastating decline of brain function, thought to be driven by the accumulation of protein debris in so-called amyloid plaques, loss of neuronal connectivity, and finally death of neurons. It seems likely that these changes begin a decade or more before the disease is first suspected.  It's a major goal of Alzheimer's research to detect the disease as early as possible, before irreversible damage to the brain has occured.
recent study from Johns Hopkins has suggested that a test for two Alzheimer's-related proteins in the cerebral-spinal fluid (CSF) may give clues that something is amiss in brain chemistry as much as 5 years before the cognitive symptoms are seen.
The new work builds on earlier observations that the CSF of patients with advanced Alzheimer's shows abnormal levels of two proteins, phosphorylated tau and beta-amyloid. These proteins are both found near sites of brain damage, so it made sense that they would be detectable in the brain fluid of these advanced patients. The new feature of the Johns Hopkins study is that these same proteins, or at least their ratios, are present in the CSF before the study population had developed symptoms of cognitive decline.
Amyloid plaques, seen here as fuzzy black blotches, in 
the brain of a person who died of Alzheimer's disease.
One of the aspects of Alzheimer's disease that was new to me  is the concept of Cognitive Reserve, that is, that some people can withstand the neuropathology similar to Alzheimer's while not showing cognitive symptoms. It is thought that the psychological flexibility or other life-long habits may improve cognitive resilience during the progression of the disease. This phenomenon makes the diagnosis of Alzheimer's disease more difficult, because each person would have a cognitive decline relative to their own baseline.  The Johns Hopkins group has seen that cognitive reserve does not associate with the proteins they measure in the CSF. Thus this approach may help reduce the uncertainty of diagnosis in patients with more advanced disease, as well as its stated goal of early detection.

Wednesday, October 16, 2013

More edible insects

The Guardian had an article this past summer saying that the foods of the future will be low on the food chain-- plants and insects. Coming from Maryland, I've always enjoyed crab, so I don't think insect
muscles wouldn't be too much of a stretch (no pun intended!) But I really can't see eating  tree grubs yet.

Friday, October 11, 2013

Collagen from dinosaur fossils-- some insight into a mechanism for preservation

Historically, fossil dinosaur bones have been considered to be entirely mineralized, that is, that they are faithful replicas of the bones but don't contain bone per se. However, in 2005, the laboratory of Mary Schweitzer fortuitously observed what looked to be soft-tissue blood vessels and even blood cells in a Tyrannosaurus leg bone. Schweitzer's lab has since worked on recovering and identifying proteins , specifically collagen, in fossilized dinosaur bones. However, many in the field find it hard to believe that 65 million-year-old proteins would survive the fossilization process, and I would say a substantial
A cartoon of collagen structure indicating major binding
or interaction sites of other proteins (shown in color). 
The protein sequences detected in fossil extracts
 all correspond to "protected" amino acids in the
 groove of the triple helix. Three out of 11 successful
reads corresponded to integrin binding sites (green).
additional group, while not actively hostile to her assertions, is at a minimum awaiting confirmation by other labs and methods. The chief issue of concern is that protein (and bone protein especially) is much more complicated chemically than RNA and DNA, making it hard to believe it could be detected in a sample millions of years old. First, in contrast to RNA and DNA, there is no way to reliably amplify protein fragments. Secondly, proteins like collagen are cross-linked, and this chemical modification complicates detection of the cross-linked portions.

Schweitzer has more recently collaborated with collagen expert Joseph Orgel in a very recent paper in the open-access jounal PLOS One, which at least offers an explanation for which protein fragments their detection methods are registering. Collagen, the major protein in bones, is wound into incredibly tough three-stranded helical fibrils, and would be as good a candidate as any to survive fossilization processes. And there are patterns to the portions of collagen detected by their experiments. Collagen fragments detected in analysis of two different fossil dinosaur bones seemed to derive from the same place in the collagen fibril, consistent with the idea that those regions are better preserved than others. Secondly, the  fragments from both species correspond to sections of collagen known to lie in the interior of the triple helix. By being shielded here, the authors hypothesize, these fragments were more likely to be preserved in sufficient amounts to be detected.
I would say that while these two factors could explain detection of fossil collagen, the same shielding and similarity effects would also apply to contaminating avian or even reptilian collagen. And it wouldn't take much modern protein contamination to drown out a 65 million year-old signal. So for myself, I still find this a tantalizing possibility, but still scientifically ambiguous.

Thursday, October 10, 2013

The social side of online gaming

Massively-multiplayer online role playing games, or MMORPGs, are popular time sinks involving very
The popular image of a gamer
long sessions in front of a computer. Popular stereotypes of gamers involve socially awkward, indoor-dwelling males subsisting on junk food and Mountain Dew.  But these stereotypes do an injustice to a huge and diverse community.  For example, World of Warcraft has 8 million subscribers including lots of folks who wouldn't fit that stereotype.
However, a lot of the scientific literature on MMORPGs examines addiction issues. Studies of huge numbers of the huge numbers of leisure players have been largely left to the marketers.
I think there's a scientific opportunity being missed here. Just as biological extracts of willow bark led to the isolation of aspirin, the strong pull and elaborate societies created online within MMORPGs are telling us something about what attracts and holds people's-- all people's-- attention. This is both a sociological phenomenon and a psychological one. The human species is tremendously, even uniquely social, and from infancy on the human brain responds preferentially to socially meaningful cues. MMORPGs are so successful because they tap into the human affinity for belonging, interaction, cooperation-- and tribalism. These games in themselves are of course creations of humans,  and their attractiveness comes in part from their large numbers of users, which makes them difficult subjects for study. The social science of online gaming will have to devise more reproducible instances which are still interesting enough to trigger the social immersion of the commercial games.

Friday, October 04, 2013

Science Magazine issue on science communication: quality control for manuscripts

Quantification of the flawed manuscript submission study. On
the left, categories of target journals. Green represents the
DOAJ list, which is suggested in the article not to vet journals  
sufficiently(see text and link). Beige represents journals on a 
blacklist maintained by Jeffrey Beale. Of the target journals,
very few of the journals which rejected the paper came from 
Beale's list, while many of the DOAJ journals did
 recommend rejection. 
This week's Science has several articles about improving communication of scientific results.  Scientific journals are in the process of a revolution driven by the world-wide web, and there are many new entrants into the field. Since scientists are under pressure to constantly publish, the dramatic increase in titles creates a possible risk to publication standards.

 An article by John Bonahan in the Science special issue focuses on quality control in open-access journals. To test how well the new journals were doing in handling manuscripts, Bonahan deliberately submitted a highly  flawed manuscript  to 304 open-access journals, and was flabbergasted to find the manuscript was accepted 157 times. Of the accepting journals, a disproportionate number came from a name and shame list maintained by Jeffrey Beall of journals which he believes are acting unprofessionally (this category would also include hidden billings and unclear copyright behaviors). However, many others which appear in the Directory of Open-Access Journals (DOAJ) also accepted the paper.
Remarkably, Beall found that four of these journals went ahead and  published the faulty manuscript even after it had been withdrawn.
This is remarkable and indicates a system of scientific discourse in distress. It is important to point out that print journals, which are not covered in this study, are also fallible, and in particular have had issues with more subtle problems like data fabrication. In fact, the blog Retraction Watch contacted Bonahan regarding his faulty manuscript study, and he said print journals were not targeted because their turnaround for manuscripts was too slow to get good numbers for his study! I think the manuscript study is thus best taken as evidence of systemic stress rather than flagging a particular publishing model as especially flawed.

Update: the Chronicle of Higher Education is more critical of the study design. I still think what Bonahan found is pretty appalling even within the limitations.

Hollow raptor teeth: evidence for a venomous bite?

A diagram of the Sinornithosaurus skull showing
grooved teeth (labelled vg) and a sinus above the
palate(labelled sff for subfenestral fossa), both of which
suggest a venomous bite.
Credit: Gong et al., 2009
The National Geographic site has an older article about evidence that at least some dinosaurs were venomous. The species in question,  Sinornithosarus, belongs to the feathered raptor dinosaurs, among which were the ancestors of birds.
Sinornithosaurus has long, spiky fangs on its upper jaw, which resemble the fangs of  "rear-fanged" snakes. These fangs additionally have grooves, and the space above the palate appears to have room for a venom gland. One important detail about these long, narrow teeth is that the creature's bite could not have been very forceful lest the teeth break (and in fact a the tip of a raptor tooth has been recovered in the fossilized wing bone of a Pterosaur). Thus this skull looks like it belonged to a creature with a bite-and-hold predation style.
This idea has remained somewhat controversial.  Grooves occur in teeth of non-venomous animals, where they can can be involved in sucking or grooming behaviors, and certainly the possibility of selective tooth wear during fossilization has to be considered. Regardless, even close relatives to Sinornithosaurus do not have these tooth grooves. So it may be that this venomous lineage was an evolutionary dead end.