Post List

  • September 29, 2011
  • 03:22 PM

September 29, 2011

by Erin Campbell in HighMag Blog

Would you rather solve a 302-piece or a 100 billion-piece puzzle? This is a question I like to throw out when I explain the power of model organisms at family gatherings. Worms have 302 neurons, while the human brain has about 100 billion (give or take a few). Today’s image is from a great example of how informative model organisms can be in understanding key processes in our bodies. Neurons are made of axons and dendrites – axons transmit information, while dendrites receive it. While both processes are key to the formation of a healthy nervous system, very little is known about dendrite formation. A recent paper describes dendrite development, using an oxygen-sensing neuron in the worm C. elegans. Kirszenblat and colleagues showed that dendrite formation in the oxygen sensory neuron is dependent on Wnt signaling, which is frequently used throughout development. Specifically, the LIN-44/Wnt signal and its associated LIN-17/Frizzled receptor trigger the initiation and guidance of the dendrite independently of axon development. Images and cartoons above show the oxygen sensory neuron (green) in normal worms (top left) and Wnt mutants (all others). Arrows point to axons while the arrowheads point to dendrites, which are either absent or incorrectly formed in the mutants.Kirszenblat, L., Pattabiraman, D., & Hilliard, M. (2011). LIN-44/Wnt Directs Dendrite Outgrowth through LIN-17/Frizzled in C. elegans Neurons PLoS Biology, 9 (9) DOI: 10.1371/journal.pbio.1001157... Read more »

  • September 29, 2011
  • 02:41 PM

Fresh water stingray facts part III: Thinking rays.

by David Lagman in Fish addict...

Now you all might think that I shall rename the blog to stingray addict but this will be the last post about rays for a while :).Rays and sharks in general is often perceived by aquarists as very smart creatures. Compared to many fishes sharks and rays have relatively large brains and in some studies, however very few, been shown to be rather smart. A large part of the brain of sharks and rays is dedicated to processing data from the Ampullae of Lorenzini which is the electro-sensory organ to locate prey. Freshwater stingrays of the family Potamotrygonidae generally have fewer of these ampullae which mean that their brains are not as large as in sea living stingrays. However their brains are still relatively large. The question is how smart are these rays really?Tool use have been observed in many lineages of the animal kingdom, such as in primates (both human and non-human), in birds and in cephalopods to give some examples. However observations of this kind have been rare in the largest group of vertebrates, namely teleost fish, until now. In a few observations members of the wrasse  family (Labridae) have been seen using stones on the sea floor as anvils while trying to crush clams. This have been observed in three different genera of wrasses so it seem to be a common method used by these fish. The first observation of tool use in wrasses was described in 1995 for the yellow head wrasse.So tool use have been observed in several species throughout the animal kingdom, and particularly in the bony fish lineage including tetrapods. The cartilaginous fish lineage on the other hand is less studied when it comes to tool use and memory studies. In 2005 a research group used five captive breed Potamotrygon castexi stingrays of the same litter to study cognitive abilities of these rays. They used a plastic tube with one white and one black painted side. On one side of the tube there was a mesh on the inside and the other side was open. Inside the tube they placed a piece of irresistible food for a stingray. The food was, due to the mesh, not accessible from one of the sides of the tube. What they observed was that the rays learned quite well that if they did the right thing they would get the food, they also learned the color on the side of the tube that was associated with the possibility to access food. The way the rays accessed the food was through blowing a jet of water into the tube to sort of flush the food out. This method, by blowing a jet of water, is used by many ray species to uncover pray hidden in the sediment. The authors of this paper suggest that this is an observation of tool use in a cartilaginous fish species, using water as a tool to access the food. However if this really is tool use is a matter of definition since its a behavior the rays are born with knowing what to do. One can however argue that in the setting with the test pipe it is in a way tool use since they need to learn to get the food out using the water. I would rather state that the paper is a good study on learning and memory in stingrays rather than an observation on tool use. In any case freshwater stingrays are very interesting and more studies on their cognition would be interesting.Kuba MJ, Byrne RA, & Burghardt GM (2010). A new method for studying problem solving and tool use in stingrays (Potamotrygon castexi). Animal cognition, 13 (3), 507-13 PMID: 20020169... Read more »

  • September 29, 2011
  • 02:36 PM

Avoid Multiple Freeze/Thaw Cycles: Wooly Bear Caterpillars

by Promega Corporation in Promega Connections

I decided to see what I could discover about my friend, the wooly bear.

The “wooly bear” is actually the freeze-tolerant final instar caterpillar of the common tiger moth Pyrrharctia isabella. These nondestructive caterpillars feed on corn, asters, birches, and sunflowers among other things. They leave their plants as third instar larvae then look for a cool, dark place, usually underneath leaf detritus to overwinter. They survive the freezing winter by producing “antifreeze” in the form of glycerol. Their super cooling point (lowest temperature they can reach without freezing) is –6° to –8°C. In the spring the hibernating caterpillars become active, eat for a few days and then each one will spin a silk cocoon from which an adult moth will emerge in about one month. From spring to fall there are usually three generations produced, and they are incredibly common in North America.... Read more »

  • September 29, 2011
  • 01:15 PM

Does a Smart Phone make Smart Science?

by Hannah Little in A Replicated Typo 2.0


A new paper in plos one, published today, has shown that experiments on human cognition needn’t be confined to the lab.
Experiments on human cognitive abilities, such as language, often rely on testing small and homogeneous groups of volunteers (mostly undergraduate students) coming to research facilities where they are asked to participate in behavioral experiments. This arrangement is not . . . → Read More: Does a Smart Phone make Smart Science?... Read more »

Stephane Dufau, Jon Andoni Dun˜ abeitia, Carmen Moret-Tatay, Aileen McGonigal, David Peeters, F.-Xavier Alario, David A. Balota, Marc Brysbaert, Manuel Carreiras, Ludovic Ferrand, Maria Ktori, Manuel Perea, Kathy Rastle, Olivier Sasburg, Melvin J. Yap, J. (2011) Smart Phone, Smart Science: How the Use of Smartphones Can Revolutionize Research in Cognitive Science. PlosOne, 6(9). info:/10.1371/journal.pone.0024974

  • September 29, 2011
  • 01:06 PM

How to tame duplicated genes

by Lucas in thoughtomics

Cell division is like an intricate dance, where chromosomes have to follow a tight choreography. The chromosomes first have to find and pair with their partners, proceed with an exchange of  DNA and then part ways again. But like the best dancers, chromosomes sometimes make mistakes. If two paired chromosomes are not lined up properly [...]

... Read more »

  • September 29, 2011
  • 11:20 AM

Improving Dementia Diagnosis With a Sleep Marker

by William Yates, M.D. in Brain Posts

Dementia presents a growing challenge for clinicians both in the assessment as well as treatment domains.  Autopsy remains the only definitive diagnostic intervention that can confirm Alzheimer's disease and the other forms of senile dementia including vascular dementia, dementia with Lewy bodies, frontotemporal dementia and other dementia variants.Since autopsy studies do not provide clinicians or their patients any direct benefits during the patient's lifetime, better diagnostic tests and clinical predictors are needed.A recent study from a team of neurologists, psychiatrists, sleep medicine specialists and pathologists from the Mayo Clinic supports the potential of a sleep disorder to aid in the diagnosis of dementia with Lewy bodies.  Lewy bodies are distinct accumulations of proteins found in the brains of individuals with parkinsonism and Lewy body dementia.  They are identified at autopsy by special stains viewed under a microscope.Dementia with Lewy bodies is often considered the second most common type of dementia.  The clinical diagnostic criteria were revised in 2005 and include core and suggestive features.  The core features include: fluctuations in cognitive abilities, parkinsonism and visual hallucinations.  The suggestive features include: sensitivity to antipsychotic drugs, reduced brain dopamine uptake on functional brain imaging and presence of the sleep disorder known as REM sleep behavior disorder (RBD).The 2005 diagnostic guidelines for dementia with Lewy bodies can be made when patients have two of the core criteria or one of the core criteria and at least one suggestive criteria.REM sleep behavior disorder (RBD) is a sleep disorder characterized by violent (or other dangerous) behavior during the REM or dream or nightmare phase of sleep.  This behavior can include punching, kicking, yelling, jumping out of bed often in response to specific content of the dream that is being experienced.  Individuals with RBD can physically injure themselves or their bed partners with their violent behaviors.In normal individuals, REM sleep includes temporary muscle paralysis preventing individuals from physically responding to dreams or nightmares.  Loss of this REM sleep paralysis can lead to development of RBD.  RBD is felt to indicate disregulation of several brain neurotransmitter systems including dopamine, serotonin and acetylcholine.  This dysregulation may explain extreme sensitivity of patients with RBD to adverse effects of a variety of psychotropic drugs including antidepressants and antipsychotics.The Mayo Clinic study included a prospective longitudinal study of a group of patients with dementia who were seen four times per year until their deaths.  Postmortem autopsies were conducted on 234 patients.  Seventy seven (33%) of the sample met pathological criteria for diffuse Lewy body disease.The authors looked specifically at RBD as a predictor of true diagnosis of dementia with Lewy body disease.  They found that RBD was three times more powerful as a predictor of Lewy body dementia than any of the the core criteria of Lewy body dementia.This study confirms the value of RBD in diagnosing Lewy body dementia--in fact it supports moving RBD up to a core feature rather than a suggestive feature.  A second multicenter study by Bliwise and colleagues has confirmed the high rates of RBD in Lewy body dementia compared to those with Alzheimer's disease.These findings should encourage clinicians to aggressively look for RBD in patients with dementia to aid differential diagnosis and the treatment planning in this challenging population.Photo of typical Santa Fe home architecture taken during sunset in Santa Fe, New Mexico from the author's collection. Ferman TJ, Boeve BF, Smith GE, Lin SC, Silber MH, Pedraza O, Wszolek Z, Graff-Radford NR, Uitti R, Van Gerpen J, Pao W, Knopman D, Pankratz VS, Kantarci K, Boot B, Parisi JE, Dugger BN, Fujishiro H, Petersen RC, & Dickson DW (2011). Inclusion of RBD improves the diagnostic classification of dementia with Lewy bodies. Neurology, 77 (9), 875-82 PMID: 21849645Bliwise, D., Mercaldo, N., Avidan, A., Boeve, B., Greer, S., & Kukull, W. (2011). Sleep Disturbance in Dementia with Lewy Bodies and Alzheimer’s Disease: A Multicenter Analysis Dementia and Geriatric Cognitive Disorders, 31 (3), 239-246 DOI: 10.1159/000326238... Read more »

Bliwise, D., Mercaldo, N., Avidan, A., Boeve, B., Greer, S., & Kukull, W. (2011) Sleep Disturbance in Dementia with Lewy Bodies and Alzheimer’s Disease: A Multicenter Analysis. Dementia and Geriatric Cognitive Disorders, 31(3), 239-246. DOI: 10.1159/000326238  

  • September 29, 2011
  • 10:15 AM

Is there anything fish don't do? Tool use!

by Daniel in Ego sum Daniel

This video and story have been making the rounds on the Internet in the last few days. I just saw it yesterday and it's fascinating! For the first time (allegedly), "tool-use" in a fish has been filmed and the behavior is available for all of us to see. The fish in question is a species of wrasse observed in Palau, Choerodon anchorago or orange-dotted tuskfish.

You can see the fish digging out a clam with its pectoral fin, then carrying it over to a rock or a coral head and cracking it with a characteristic sideways motion of the head. The fish was observed doing this three times in a row, the last of which was recorded. Each event lasted less than five minutes. Here are summaries of the story from Scientific American, Science Daily and AnimalWise.

This finding is being published as a short notice in the journal Coral Reefs and joins other findings from earlier this year, published in the same journal, presenting the first photographic evidence of the same behavior in another species of tuskfish, Choerodon schoenleinii. That story was summarized in Science Now and Wired Science. In fact, there have been a handful of reports of the same behavior from different species of wrasse indicating that this might be a shared ancestral behavior in the Labridae.

Whether this constitutes "real" tool use as seen in mammals and birds, or not, will depend entirely on the kind of definition you use. That question is boring to me. But I do think it would be a mistake to equate or compare this "tool use" in fish to, for example, tool use in chimpanzees. Instead I think the interesting perspective is to put this behavior within the already known complex feeding and food seeking behaviors in fish to see in which niches "tool use" might have been beneficial.

Bernardi, G. (2011). The use of tools by wrasses (Labridae) Coral Reefs (Online First™, 20 September 2011) DOI: 10.1007/s00338-011-0823-6

Jones, A., Brown, C., & Gardner, S. (2011). Tool use in the tuskfish Choerodon schoenleinii? Coral Reefs, 30 (3), 865-865 DOI: 10.1007/s00338-011-0790-y

... Read more »

  • September 29, 2011
  • 10:03 AM

Aim Your Damages, And Your Case, at "The Golden Mean"

by Persuasion Strategies in Persuasive Litigator

By Dr. Ken Broda-Bahm - Aristotle, the original philosopher of communication, wrote in The Nicomachean Ethics about "the Golden Mean, " or the idea that virtue is often a happy medium between two vices (for example, courage is the virtue wedged between the vices of recklessness on the one hand, and cowardice on the other). More recently, Dennis Elias, an influential voice in the field of trial psychology, wrote in his blog, JuryVox, about current research showing that this thinking also applies to damage requests in litigation: When a requested amount is framed as a reasonable mid-point between two unreasonable...

... Read more »

Rodway, P.; Schepman, A.; . (2011) Applied Cognitive Psychology. info:/

  • September 29, 2011
  • 08:19 AM

Mass Grave of Children in Peru

by Katy Meyers Emery in Bones Don't Lie

Earlier this month, archaeologist revealed a large mass grave containing the remains of children and llamas. The grave was found on the coast of Peru, near the ancient Chimú capital of Chan Chan. The 800 year old grave contains the remains … Continue reading →... Read more »

Centurion, Curo, and Klaus. (2010) Bioarchaeology of human sacrifice: violence, identity and the evolution of ritual killing at Cerro Cerrillos, Peru. Antiquity. info:/

  • September 29, 2011
  • 06:30 AM

Reducing Unnecessary Hospitalizations of Nursing Home Residents

by Rogue Medic in Rogue Medic

Today in the New England Journal of Medicine there is a perspective piece on something near, and dear, to all of our hearts - unnecessary hospital admissions from nursing homes.

A lot of nursing home patients could be treated on site, without calling an ambulance to take them to the ED (Emergency Department) to produce large bill, but maybe not any better care.... Read more »

Joseph G. Ouslander, M.D., and Robert A. Berenson, M.D. (2011) Reducing Unnecessary Hospitalizations of Nursing Home Residents. N Engl J Med , 365(September 29, 2011), 1165-1167. info:/

  • September 29, 2011
  • 05:59 AM

Why Brain Scanners Make Your Head Spin

by Neuroskeptic in Neuroskeptic

Here at Neuroskeptic we see a lot of dizzyingly bad (and sometimes even good) neuroscience, but did you know that brain scanners can literally send your head into a spin? A new paper explains why, with implications for all MRI researchers.MRI scanners rely on extremely powerful magnetic fields. This is why you can't take metal objects into the scanner room, as they'd be pulled into it. Yet the fields can also exert other kinds of effects on the body.I'd always been told that static, unchanging magnetic fields are biologically inert. But moving through the field too quickly can cause side effects. When an object moves through a magnetic field, induction happens - electrical currents are produced.In the case of the human body, these small currents can activate nerve cells. Depending on which cells they hit this can cause you to feel dizzy, see flashes of light, experience tingling sensations, and so on. Or so I thought.However, a new paper from Dale Roberts et al of Johns Hopkins shows that just being in a powerful magnetic field can cause dizziness and vertigo - with no movement required. They noticed that lying still in or near an MRI scanner causes nystagmus, abnormal horizontal eye movements, and that the amount of eye movement is directly correlated with the angle at which the head is positioned relative to the field.The nystagmus was caused by an automatic reflex in response to effects in the vestibular ("balance") system of the ear. Roberts et al realized that the static magnetic field causes electrical currents that activate vestibular cells, even when the head is perfectly still. It happens because there's a natural flow of electrically charged ions into these cells in a part of the ear called the semicircular canal. The magnetic field interacts with this ion current, in what's called a Lorentz force.The semicircular canals normally allow us to sense when our head is moving. Our eyes automatically compensate for head movement to keep us looking in the same direction. The MRI magnet fooled the ear into thinking the head was rotating, and the eyes produced nystagmus as a result.Two patients who had suffered damage to their semicircular canals were immune to the effect.This has important implications for functional MRI studies of brain function. Many people are interesting in measuring eye movements during MRI scans. This finding suggests that these movements may be unusual, compared to normal eye movements outside the scanner. Worst, the vestibular stimulation could alter brain activity:Vestibular stimulation induced by the magnetic field in healthy subjects simply lying in the bore could activate many brain areas related to vision, eye movements, and the perception of the position and motion of the body.Roberts, D., Marcelli, V., Gillen, J., Carey, J., Della Santina, C., & Zee, D. (2011). MRI Magnetic Field Stimulates Rotational Sensors of the Brain Current Biology DOI: 10.1016/j.cub.2011.08.029... Read more »

Roberts, D., Marcelli, V., Gillen, J., Carey, J., Della Santina, C., & Zee, D. (2011) MRI Magnetic Field Stimulates Rotational Sensors of the Brain. Current Biology. DOI: 10.1016/j.cub.2011.08.029  

  • September 29, 2011
  • 12:30 AM

What is the Role of the Long Head of the Bicep Tendon?

by Stephen Thomas in Sports Medicine Research (SMR): In the Lab & In the Field

Su et al used 10 cadaver shoulders to examine the amount of humeral head displacement following varying degrees of anterosuperior (i.e., supraspintatus subscapularis) and posterior/superior (i.e., supraspintus infraspinatus) rotator cuff tears when loaded in a posterosuperior direction. ... Read more »

Su WR, Budoff JE, & Luo ZP. (2011) Posterosuperior Displacement Due to Rotator Cuff Tears. Arthroscopy : the journal of arthroscopic . PMID: 21908156  

  • September 28, 2011
  • 06:13 PM

Hendra Virus

by James Byrne in Disease Prone @SciAmBlogs

In recent months Australia has seen the lengths science will go to to control the potential outbreak of significant infectious diseases. At this stage Hendra virus is not particularly infectious in humans but is very deadly and some important recent developments have led to increased concern in the scientific community.... Read more »

  • September 28, 2011
  • 05:42 PM

Women better at judging men’s sexual orientation near to ovulation

by Psych Your Mind in Psych Your Mind


Living in the San Francisco Bay Area provides many benefits: good food, great activities, incredible landscape. For me, however, the Bay Area is SOO special, because it caters to a fabulously diverse array of residents. For example, each year San Franciscans can take to the streets to herald in spring during the Cherry Blossom Festival in Japantown, celebrate the beauty of leather during Folsom Street Fair, or stomp their feet and slap their thighs to the music at the completely free – Hardly, Strictly, Bluegrass. The variety of interests, cultures, traditions, and values in the Bay Area is a beautiful thing.
One interesting result of this diversity is that single, female San Franciscans are not often surprised when a man they’ve been eyeing all night, leaves the bar, with his boyfriend, not his girlfriend. San Francisco is, after all, home to The Castro - one of America’s first and arguably the best known, gay neighborhoods. Perhaps over the years women in San Franscisco have become especially adept at judging who is straight from who is gay (or who falls somewhere along the continuum). Interestingly, however, recent research has shown that women’s accuracy in judging male sexual orientation does fluctuate. Not by city (though someone should do that study) but instead by fertility (ability to conceive) across the menstrual cycle. Here’s the study…
Read More->... Read more »

  • September 28, 2011
  • 04:41 PM

Promiscuous girl? Blame her parents.

by NerdyOne in Try Nerdy

Picture the scene: the heartbroken guy exclaims, “I can’t believe you cheated on me! And with four other guys! Why?! How could you do this?” and the accused girl uses the old fallback, “Well, y’know, my parents are second cousins.”

…Okay, so that’s not an old fallback yet, but research in the latest issue of Science makes me think that it’s not a future impossibility.

In today’s post, find out what researchers have been doing to suggest that inbred females may have a propensity for promiscuity (The Jerry Springer Show, anyone?).... Read more »

Michalczyk L, Millard AL, Martin OY, Lumley AJ, Emerson BC, Chapman T, & Gage MJ. (2011) Inbreeding Promotes Female Promiscuity. Science (New York, N.Y.), 333(6050), 1739-1742. PMID: 21940892  

  • September 28, 2011
  • 03:16 PM

Resilience from a Psychological Perspective

by Daniel Dumke in SCRM Blog - Supply Chain Risk Management

Resilience developed to one of the dominating concepts in supply chain risk management and this review takes a different look on corporate resilience by viewing it from a psychological perspective.... Read more »

Coutu, D.L. (2002) How Resilience works. Harvard Business Review, 46-55. info:/

  • September 28, 2011
  • 02:18 PM

A flawed study claiming prevention of Lyme spirochete infection with topical antibiotics

by Microbe Fan in Spirochetes Unwound

Two recent papers tested the effectiveness of topical antibiotics in preventing Borrelia burgdorferi infection in mice following a tick bite.  Infection by the Lyme disease spirochete was successfully halted in the Knauer et al. study from Germany1 but not in the Wormser et al. study conducted in New York.2  However a flaw in the Knauer study may have unfairly tipped the outcome in the antbiotic's favor.  (I'll save the Wormser study for another post.)The paper by Knauer and colleagues1 presented two trials, which differed in how the mice were inoculated with B. burgdorferi,  In the first trial the spirochetes were injected into the skin, and azithromycin was applied topically one hour, three days, and five days later at the injection site.  In the second trial infected ticks transmitted the spirochetes to the mice.   Azithromycin was applied topically to the feeding site immediately after the ticks stopped feeding.  In both trials azithromycin was dissolved in ethanol for application to the inoculation site.  Disseminated infection of the mice was assessed by culturing the heart, bladder, ear, and tarsus 56 days after inoculation.The results from the first trial reveals the problem with the study (Table 1).  Among the ten mice in the placebo group (first row), which received only ethanol, only one (10%) had any culture positive organs 56 days later.  The spirochetes failed to establish a persistent infection in the other nine mice, suggesting that the investigators were working with a weakened strain of B. burgdorferi.  The ethanol could have had a slight killing effect (see the second trial) yet could not have accounted for the poor infection rate in the placebo group.The table legend claims that the difference between the placebo and treatment groups was significant, but the statistics were done on the numbers in the column labeled "Infection Status."  According to the text of the paper, "Infection Status" refers to those animals that managed to produce antibodies against B. burgdorferi antigens.  Infection status is therefore not the proper metric to assess the infectivity of B. burgdorferi.  When the statistic are performed with the appropriate numbers, located in the column under "Culture," the effect of azithromycin (1/10 culture positive in control group vs. 0/10 culture positive in any treatment group) is not significant (P = 0.9 for control vs. any treatment group).Results from the second trial are shown in Table 2.  This trial included an extra control group that did not even receive ethanol.  Four of the seven mice in the untreated group (57%) ended up culture positive.  This is still a low infection rate compared to the rates observed in other studies, in which 90-100% of the control animals end up infected following tick inoculation of B. burgdorferi.  Two of the nine mice treated with ethanol alone (placebo) were culture positive, suggesting that ethanol alone helps prevent infection (57% culture positive in "no treatment" group vs. 22% in placebo group, P = 0.152), although the experiment would need to be repeated with larger groups of animals to make a statistically convincing case.None of the animals treated with azithromycin were culture positive.  However the number of animals was again too low to conclude that antibiotic treatment was effective (2/9 culture positive in placebo group vs. 0/9, 0/8, and 0/5 in the treatment groups, P > 0.4 for comparison of each treatment group with placebo group).  The authors were able to claim statistical significance by combining the two control groups (no treatment and placebo) and the treatment groups.  However it is inappropriate to combine groups in this manner to attain statistical significance.Even if the investigators had used a larger number of animals, the problem of their weakened challenge strain remains.  Application of topical antibiotics may turn out to be effective in preventing Lyme disease after a tick bite, but the study presented by Knauer and colleagues was not a fair test of this treatment approach.References1. Knauer, J., Krupka, I., Fueldner, C., Lehmann, J., & Straubinger, R. (2011). Evaluation of the preventive capacities of a topically applied azithromycin formulation against Lyme borreliosis in a murine model Journal of Antimicrobial Chemotherapy DOI: 10.1093/jac/dkr3712. Wormser, G., Daniels, T., Bittker, S., Cooper, D., Wang, G., & Pavia, C. (2011). Failure of topical antibiotics to prevent disseminated Borrelia burgdorferi infection following a tick bite in C3H/HeJ mice Journal of Infectious Diseases DOI: 10.1093/infdis/jir382... Read more »

  • September 28, 2011
  • 01:09 PM

The Orange-Dotted Tuskfish Strikes Back: Movie Shows New Species of Fish Using Tool

by Paul Norris in AnimalWise

Recently, the blackspot tuskfish (Choerodon schoenleinii) became a media sensation when it was captured in photos using a rock as tool to open a clam. Apparently not happy with the print media attention afforded to its relative, the orange-dotted tuskfish (Choerodon anchoago) has taken the behavior to the movies … Continue reading →... Read more »

  • September 28, 2011
  • 09:42 AM

Where to put Australoithecus sediba?

by Eric in APE

It took me some time to decide what I should do with Australopithecus sediba on this Blog, in the end I decided to concentrate on the aspects I at least know a little bit of, one of them is taxonomy.I had to reconstruct a bunch of phylogenetic trees in the last few months and I found a someof free online tools which enabled me to do this without using any fancy (and expensive) Computer Programs. The only disadvantage of these resources is that they were originally made for molecular data sets. This made my work a little bit more complicated since I had to modify my morphological datasets in a way that these programs were able to work with them. I won’t talk about the exact process right now; instead I want to show you some of the stuff I did with Australopithecus sediba.First of all, let’s have a look at a classic tree which illustrates the phylogenetic relationships among the genus Homo. I took the Tree from Strait et al. (1997) for this particular example:Strait et al. (1997)There’s nothing really special about this tree, sure you could discuss whether or not the shown phylogeny represent the true relationships of these fossils, but discussing this stuff always tends to get boring, since you have to look at the characters and you need to discuss the validity of each of themTo make things a little more interesting, I took the character matrix from Strait et al. and included Australopithecus sediba. The characters for Australopithecus sediba were taken from the initial description of this Fossil (Berger et al., 2010). This is the tree you get, when you run this modified matrix through an Analysis:Same character matrix but with A. sediba.Sediba ruined everything!What in the first tree looked like a nice and clear relationship is now collapsed into something completely indifferent.To make things clear, the taxonomic position of Homo habilis and Homo rudolfensis never was pretty clear. In fact, the latter species was established, because the initial hypodigm (the total sum of all fossils which describe a species) of Homo habilis was so diverse in its morphology that it was split up into two separate species. The “new” species was then called Homo rudolfensis. I won’t talk up the exact reasons why this was the case, since it would make this post too long, but I will eventually come back to this topic in another post.Let’s go back to Australopithecus sediba for the moment. It’s not only that the fossil practically ruins the common taxonomic picture of relationships of early homo, it’s also very young. Right now, Australopithecus sediba is dated at about 1.9 million years, this is very young, if you keep in mind that there are fossils of Homo habilis and Homo rudolfensis which are much older then 2 million years. There are also possible fossils from Homo ergaster/erectus which are only slightly younger then the sediba fossils. Now add the about 1.7-1.8 million year old remains from Dmanisi/Georgia to this mess and you can see how complicated this whole story starts to look.Fortunately the tree I showed you at the beginning of this post isn’t completely useless since it shows that Australopithecus sediba falls somewhere within the relationship of Homo ergaster/erectus, Homo rudolfensis and Homo habilis. So let’s have look at the possible relationships and the possible consequences of each scenario: Scenario if A. sediba would share a LCA with the Genus Homo In this scenario, Australopithecus sediba would share a last common ancestor with the Genus Homo. The only problem which arises from this tree is that you have to discuss what you should do with the Homo rudolfensis and habilis fossils which pre-date the emergence of Australopithecus sediba in the fossil record.All other scenarios basically ruin our contemporary picture of the Genus Homo: Two of the possible relationships if A. sediba would be place somewhere within the Genus Homo   No matter which scenario we look at, none of them shows the Genus Homo as a monophyletic group. This means that either we have to include Australopithecus sediba within the genus Homo which I’m not very fond of since it would lead to an even weaker definition of it. Or we have to exclude Homo habilis and/or Homo rudolfensis from the genus Homo. The Genus Homo would then begin with Homo ergaster/Homo erectus and everything before that species would be either inside the genus Australopithecus or in a complete new genus.Personally, I have no Idea what I should make out of this stuff. Right now everything seems to contradict itself and I think we need to have much more knowledge about this certain period of time. This means of course more fossils from this period but also more research on the already known fossils.What I think we can safely right now is that the emergence of the genus Homo didn’t happen in a gradualistic fashion where one species slowly evolved into the next one. I think what we have here is a series of, possible independent, speciation events. This would explain why we have that many species that look similar to another but who overlap in spatial as well as temporal aspects and whose phylogenetic relationships are completely unclear. I have some more thoughts on this matter and I will write another Post where I go into much more detail. For now, all I can say is that, although Australopithecus sediba completely ruins the contemporary phylogeny, it might help us to really understand what happened back then.References: ... Read more »

Berger, L., de Ruiter, D., Churchill, S., Schmid, P., Carlson, K., Dirks, P., & Kibii, J. (2010) Australopithecus sediba: A New Species of Homo-Like Australopith from South Africa. Science, 328(5975), 195-204. DOI: 10.1126/science.1184944  

Strait, D., Grine, F., & Moniz, M. (1997) A reappraisal of early hominid phylogeny. Journal of Human Evolution, 32(1), 17-82. DOI: 10.1006/jhev.1996.0097  

  • September 28, 2011
  • 09:17 AM

Tip of the Week: Introduction to R Statistical Software (with video)

by Mary in OpenHelix

This week’s video tip is different from our usual tips in several ways. First, you won’t hear me–this webinar was done by Heather Merk of Ohio State. We also usually highlight web-based tools, and this presentation on R statistical computing tools relies on the command line. And it’s longer than we usually do–but because of [...]... Read more »

Blankenberg, D, Von Kuster, G, Coraor, N, Ananda, G, Lazarus, R, Mangan, M, Nekrutenko, A, & Taylor, J. (2010) Galaxy: A Web-Based Genome Analysis Tool for Experimentalists. Current Protocols in Molecular Biology, 19(10). DOI: 10.1002/0471142727.mb1910s89  

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