The Colors of the Dinosaurs

Research published today in Nature describes the discovery of melanosomes in fossils of several non-avian dinosaurs.

Melanosomes are melanin-containing organelles found in the feathers of birds, and responsible for the colors of those feathers. Researchers looked at the fossils of several non-avian dinosaur species possessing integumentary filaments which had previously (and controversially) been categorized as feathers. The controversy stemmed from the classification of these filamentous structures as feathers, with some researchers contending that the structures were degraded dermal collagen fibers, and not feathers at all.

Seeking to resolve this issue, Zhang et al examined the fossils using a scanning electron microscope, finding evidence of "sub-micrometre-sized bodies" that they interpret as fossilized melanosomes. Furthermore, the researchers identify the specific color associated with the fossilized melanosomes: a reddish-brown to yellow pigment.

Much of the letter is spent providing evidence to back up the claim that the identified structures are melanosomes, and it will be up to the experts to battle out a consensus. But based on their research, Zhang et al conclude the confirmation of the putative evolutionary precursors of true feathers, and the broach the possibility of decoding the external coloration of the dinosaurs. Indeed, the authors suggest some color schemes in the letter:

"Only phaeomelanosomes have been identified so far in filaments from the tail of Sinosauropteryx, and this suggests that the dark-coloured stripes along the tail in the fossil, and possibly also the filamentous crest along the back, exhibited chestnut to rufous (reddish-brown) tones."

For more details of their research, and more potential dinosaur color schemes, the article is available online:

Zhang et al. Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds. Nature advance online publication 27 Jan 2010. doi:10.1038/nature08740

Image by Chuang Zhao and Lida Xing, courtesy of The Guardian, here.

Research Roundup: Grid cells, social value, migranes, fraud

Here's a collection of 3 recently published studies that caught my eye and one recently published case of massive scientific fraud. The Neurophilosophy Blog writes up a recent paper about the discovery of grid cell-like activity in humans. Spoilers: Researchers recorded activity very similar to that of mice grid cells. But with data collected only through population imaging, direct electrophysiological measurements are needed to show the existence of human grid cells.

Updated: Link to the original paper, published today in Nature.

Nature Neuroscience published a brief communication regarding activation of the dorsal amygdala in response to perceived inequality in subjects adverse to such inequality. See the paper for a better description of their methods and conclusions.

Another Nature Neuroscience article describes the neural mechanism behind exacerbation of migrane headaches by light. Spoiler: It's due to posterior thalamic neurons. These neurons receive nociceptive signals from cranial dura mater, but their activity is modulated by projections from retinal ganglion cells. So the light information modulates the nociceptive signal being passed through the thalamus to layers I-V of somatosensory, visual, and associative cortices.

Meanwhile, over at the journal Acta Crystallographica Section E, an editorial published last month reveals some extensive scientific frauds involving papers published during 2007. The editorial states that at least 70 structures were falsified, and that the number of structures will most likely rise. Credit for the discovery goes to Ton Spek. The basis of the fraud involves using a real set of data from a correctly determined structure to produce multiple papers wherein authors changed one or more atoms in the structure to produce a new, wholly imaginary compound. At most, more than 18 fraudulent structures were composed from a common data set.

The editorial states:

"The correspondence authors are Dr H. Zhong and Professor T. Liu, both from Jinggangshan University, Jian, China. The co-authors on these papers included other workers from Jinggangshan University together with authors from different institutions in China. Both these correspondence authors and all co-authors have signed forms agreeing to the retraction of 41 papers published by Dr Zhong and 29 by Professor Liu. Details of these retractions appear elsewhere in this issue of the journal. Having found these problems with articles from Jinggangshan University, all submissions from this University to Acta Crystallographica Sections E or C have now been identified and are being checked for authenticity. Preliminary results indicate that further retractions will result from this exercise."

Editorial by Willian T.A. Harrison, Jim Simpson, Matthias Weil. Acta Crystallographica Section E Structure Reports. Vol 66, pages e1-e2. Jan. 2010. via @bengoldacre

John Cleese Explains Neuroanatomy

I've spent quite a lot of time over the past couple of weeks listening to neuroanatomy lectures. Now, thanks to Vaughan over at Mind Hacks, and @brainshow, I'll probably spend the next couple of weeks wishing that my neuroanatomy class was being taught by John Cleese. Another hopeless dream is born. The Brain as Explained by John Cleese.

Bat and Whales: echolocation siblings

Yesterday, my eye was caught by a post written by Ed Yong over at Not Exactly Rocket Science about two recent studies showing that the echolocational abilities of bats and whales are both based on the same 14 amino acid changes to a single gene, Prestin. It can be universally acknowledged that morphologically, phenotypically, and geographically, bats and whales are highly dissimilar species. Yet both bats and toothed whales use echolocation for navigation in environments hostile to more traditional photon-based sight. And although the exact mechanisms behind the ability of echolocate are different in bats and whales (as might be expected given the dissimilar physiologies and habitats), the two groups share a strong genetic similarity in Prestin. So strong, in fact, that a phylogeny drawn using the DNA sequences of Prestin places all echolocating mammals as close relatives, excluding established evolutionary relatives such as other bats and whales who do not echolocated.

This case of convergent evolution is made more interesting because of the extreme behavioral differences in the way whales and bats practice echolocation. Bats echolocate through the medium of air, creating their sonar pulses via their voicebox. Whales echolocate through water by passing air through their nasal bones. These mechanistic differences are too great to be encoded by a single similar genes. Indeed, Prestin does not per say confer the ability to generate echolocation signals upon bats and whales. Instead, Prestin confers the ability to detect the rebounding echos, altering outer hair cells to make them more sensitive to the ultrasonic frequencies used in echolocation. With their enhanced ability to detect high frequency sounds, bats and whales evolved distinct physiologies to generate those sounds, as mediated by the demands of their distinct environments.

As Ed Yong points out, the independent replication of such distinctive genetic changes, resulting in the generation of distinct mechanisms to take advantage of the shared ability, is frankly astounding. Yet again, convergent evolution reinforces the duality of beautiful complexity and mysterious simplicity in the natural world.

Echolocation in bats and whales based on same changes to same gene. By Ed Yong at Not Exactly Rocket Science.

The original papers:

Liu et al. Convergent sequence evolution between echolocating bats and dolphins. Current Biology: 20, R53-R54 (2010).

Li et al. The Hearing Gene Prestin Unites Echolocating Bats and Whales. Current Biology: 20, R55-R56 (2010).

Using brain imaging to diagnose PTSD

Last week, I came across a paper entitled "The synchronous neural interactions test as a functional neuromarker for post-traumatic stress disorder (PTSD): a robust classification method based on the bootstrap". I've been mulling over whether to blog about this paper; on one hand, it presents some interesting conclusions, which I greet with some degree of skepticism. On the other hand, having training neither in human brain imaging, psychology, or post-traumatic stress disorder, I was loath to make any statements regarding the paper and it's conclusions.

However, after reading the paper, and discussing its existence with a number of people, I've decided to publish a post (this one) asking for the opinions of those readers who do know enough about the subject and the methodologies utilized to comment on the validity of the papers conclusions. Below I will describe the paper's methods, its conclusion, and a link to the article. Please, comment on the paper and its conclusions.

The paper, by Georgopoulous et al, published in the Journal of Neural Engineering, describes the use of magnetoencephalographic (MEG) recordings to diagnose PTSD. Recordings of synchronous neural interactions (SNI) were made while asking subjects to fixate on a spot of light for 60 seconds, allowing the researchers to "engage the brain in a stable condition". The recorded data were analyzed using "bootstrap-based analyses". The paper explains the choice to use a bootstrap-based analysis:

"This approach was motivated by the common practical situation where a ‘new’ subject S needs to be classified, given subjects of known condition, i.e. belonging to a control (i.e. non-PTSD) group C or to the PTSD group D."

Using their analysis, which is detailed in the paper, the authors claim they can successfully differentiate subjects suffering from PTSD from healthy control subjects with greater than 90% accuracy.

Conclude the authors:

"Altogether, these findings document robust differences in brain function between the PTSD and control groups that can be used for differential diagnosis and which possess the potential for assessing and monitoring disease progression and effects of therapy."

A note: although all PTSD subjects were veterans, not all were suffering from PTSD induced by military trauma. Some were affected due to childhood trauma or non-military trauma during adulthood. Given the differences in the causation, is it reasonable to expect that all suffers of the disorder would display distinguishable synchronous brain activity differences? Certainly, I do not find it impossible that the data could show differences in brain activity when comparing PTSD sufferers from healthy controls. But in my mind, a diagnostic tool is most useful if it can differentiate one psychological issue from another. Is it reasonable to expect that a patient will either have PTSD, or be completely psychologically normal? I wonder about the selectivity of  the SNI test. Can it differentiate between PTSD and any one of the myriad of psychological issues that can affect the human brain (especially following military service). The ability to distinguish between shades of grey, instead of black versus white, must be the final goal of any psychological diagnostic tool.

As previously mentioned, due to my inexperience with brain imaging and mathematical techniques of analyzing such data, I cannot comment of the use of the bootstrap analysis. Is there someone out there willing to read the paper and provide an analysis?

Georgopoulous et al. The synchronous neural interactions test as a functional neuromarker for post-traumatic stress disorder (PTSD): a robust classification method based on the bootstrap. J. Neural Eng. 7 (2010). doi:10.1088/1741-2560/7/1/016011

Updated 1/25/2010: Have just seen that Vaughan Bell over at Mind Hacks wrote on the 24th about this article, brining up that same issue regarding the scan's ability to separate PTSD from normal, as opposed to PTSD from another disorder.

Annual Online Consciousness Conference

For those interested in discussing questions of consciousness: the Second Annual Online Consciousness Conference has been scheduled for February 19th-March 15h. The conference format is as follows: papers/commentary by invited commentators will become available two weeks before the conference (on February 5th). During the conference, the authors of the posted papers will discuss their papers with conference attendees in the online comments sections. Session topics include: Higher Order Consciousness, State of the Art in Brain Decoding, Inner Psychophysics: Correlates, Causes and the Neurobiology of Consciousness, Color Consciousness Conceptualism, Ghosts and Sparse Properties and many other.

Not being too familiar with researchers in the field of consciousness, I only recognize David Chalmers among the list of invited commentators. The full lists of the session topics and invited commentators is available online.

The host blog, Conciousness Online, was founded by Richard Brown. According to their website, the goal of the blog is:

" to bring consciousness researchers together in an online venue to promote widespread discussion and exchanging of views/data related to the scientific and philosophical study of consciousness, broadly construed."

NPR Interview: Darwin's Great-Great Grandson

Last evening, I happened to turn on NPR to hear Terry Gross of the program Fresh Air interviewing a man called Randal Keynes. Mr Keynes is a great-great grandson of Charles Darwin, who has written a book about Charles Darwin, the death of Darwin's first daughter, and the composing of the Darwin's theory of evolution. The book, entitled Darwin, His Daughter, and Human Evolution, is the book upon which the film Creation (recently mentioned on this blog) is based.

The NPR interview is available online in audio form (the transcript is also available).

Darwin, His Daughter, and Human Evolution. by Randal Keynes, at amazon.com

The Poison in the Platypus

Snakes and spiders are the classic venomous animals. But producing toxic venom is not the exclusive ability of reptiles and arachnoids.

But a very small number of mammalian species also posses toxic venom, including the male platypus.

However, although the clinical signs of platypus venom are well known (excruciating pain, rapid swelling, hyperalgesia), many of the phenotypic effects have not been matched to chemical players with specific cellular/molecular interactions. Now, research published in the Journal of the American Chemical Society identifies a peptide that is highly concentrated within platypus venom, and matches that peptide to previously reported cellular consequences of venom injection.

Previous research has identified a number of platypus venom constituents, including defensin-like peptides, C-type natriuretic peptides (OvCNPs),NGF, and hyaluronidase. Additionally,  previously research from the lab of Daisuke Uemura of the Nagoya University showed that crude platypus venom induces a potent influx of calcium into human neuroblastoma cells. Now, Masaki Kita and colleagues have expanded on that research, identifying Heptapeptide 1 (a primary component of venom fluid) as the main effector of this calcium increase.

They attempted to identify the mechanism of this increase, testing for binding of heptapeptide 1 to L- and N- type voltage gated calcium channels, potassium channels (Ka, Katp, or hERG), or sodium channels. Heptapeptide 1 did not bind to any of these channels, leading Kita et al to conclude that heptapeptide 1 "may specifically bind to other receptor channels or biomacromolecules, such as GTP-binding regulatory proteins, as in the case of the direct activation of G_i proteins by mastoparan or substance P."

Additionally, they conclude that the influx of calcium was not caused by a the high concentration of heptapeptide 1 (which is found in concentrations of 200 ng/uL within the venom), but rather by specific interactions with target molecules. What those molecules are is a mystery to be reveled in another paper.

One evolutionary curiosity: the defensin-like peptides found within the platypus venom are also found within reptile venom. However, genetic analysis in 2008 revealed that the platypus peptides evolved independently from the reptile peptides, although both were derived from the same gene family.

NYTimes article about the research, including a (highly approved of by this author) reference to a literary example of platypus poisoning.

The original article: Kita et al. Duck-Billed Platypus Venom Peptides Induce Ca²⁺ Influx in Neuroblastoma Cells. J. Am. Chem. Soc. 2009, 131: 18038-18039. DOI: 10.1021/ja908148z

Update 1/25/2010: To clarify a question brought up while discussing this blog post: the venom is released from spurs located on the platypus' hind legs.

A Different Kind of McCarthyism

I've been reading a lot about Jenny McCarthy's assault on Autism science recently, (eg. Wired's recent cover story), but her latest, as reported by Jeremy Radford at Discovery News, makes it very clear that this is not just about distrust of doctors or wariness of over-vaccination. It is a fundamental distrust or disbelief in science. Here's the main face-palm moment:

McCarthy dismissed the latest scientific research as worthless, and the scientists who conduct autism research as incompetent: "We're the ones seeing the real results. And until doctors start listening to our anecdotal evidence, which is, ‘This is working, it's going to take so many more years for these kids to get better. Every parent will tell you something different that helped their child."

It's a bit unfortunate to make my first post such a disturbing one, but this is one of the more tragic and frustrating neuroscience-related stories that's been in the media recently, so it's been on my mind and I thought I'd share and see if anyone can eke more perspective out of this than I can...

In his article, Radford delves right to the core of why this quote is so disturbing, pointing out that "McCarthy, like many non-scientists, seems to think that stories and anecdotal evidence are just as good as -- if not superior to -- well-controlled scientific studies." And reading the comment thread on his article just proves his point. Some (perhaps many) people do not understand the power of the scientific approach or appreciate its benefits, and misunderstanding leads to mistrust.

A common complaint against science is the accusation of fallibility (scientists are just people - they make mistakes like the rest of us) or the suspicion of political motivation (they have an agenda to manipulate their data)... I think that there is actually a disturbing and difficult grain of truth here. It is true, is it not, that few scientists would assert that any published study should be taken at face value? We all assess the articles we read to determine how much we trust their methodology, and we know that every scientist is tempted to try to support their own pet story, as much as they try to be objective.

So the question is, what are we asking non-scientists to do? We talk about science education, and it's true that even the most basic education could help avoid the kind of drivel McCarthy spouts above. However, somehow I can't bring myself to believe that science education will ever allow the common man or woman to read a study in Pediatrics and understand all the methodology and conclusions, to really be able to assess the reliability of the source. So aren't we really asking people to take a sort of leap of faith? To trust that science has all the answers and should be trusted in all cases above other sources, even when you don't understand it? Maybe so... Or maybe I'm too pessimistic about what education can accomplish.

Anyway, I'm realizing I don't have a conclusion here. I agree that we need to focus on educating the public, but I think we need to think long and hard about what we need to teach them. There is a fundamental gap out there. We can't just hope to fill it by pouring in knowledge from on high, because it is also a gap of language and a gap of belief and a gap of trust. We need to engineer a bridge built of all these things if we can hope to leave ignorance behind. If we can hope to.

Fun with Mathematics, in Britain

Although not strictly neuroscience related, the following exchanges are suitably entertaining to warrant spreading. In one corner, we have a Mr. Tom Brooks whose research is reported in British news (Metro and Daily Mail). Mr. Brooks has analysed 1,500 prehistoric monuments, finding that they lie on a grid of isosceles triangles, with the tip of one pointing to the next, and so on. Mr. Brooks research therefore clearly shows (according to Mr. Brooks) that prehistoric residents of Britain 1) had advanced understanding of geometry 1,000 years before it was invented by the Greeks  and 2) used that knowledge to construct monuments allowing them to travel between settlements easily. Says Mr. Brooks:

"Such patterns could only have been the work of intelligent surveyors and planners, which throws into question all previous claims as to the origin of mathematics."

However, Mr. Brooks points out that the work involved was most likely far outside the abilities of the members of the primitive culture that have been previously associated with the monuments in question. He suggests that this discrepancy points to "a culture existing in these islands in the past quite outside our expectation and experience today".  According to Ben Goldacre, writing for his blog Bad Science, Mr. Brooks does not rule out extraterrestrial aid.

Perhaps the monuments are in fact landing pads for alien spaceships, left over from when aliens enslaved the human race, posing as gods, before vanishing into the universe, to plot and scheme amongst themselves, until their empires were intruded upon by a small band of humans who traveling through a device known as a Stargate...

Anyway, many people have pointed out that given a sufficiently large data set (and 1,500 monuments is satisfyingly large), many kinds of patterns can be "discovered".

To prove this point with style, grace, and snark, is Matt Parker. Mr. Parker, who hails from the School of Mathematical Sciences at Queen Mark University of London, applies the same techniques used by Mr. Brooks to study another ancient and mysterious structure: Woolworth grocery stores. The pure genius of Mr. Parker should not be distilled, and his whole essay can be read online on Ben Goldacres other blog.

But as a spoiler, here is Mr. Parker's introduction to his research, and his conclusion:

“We know so little about the ancient Woolworth stores, but we do still know their locations” explains Matt Parker, “so I thought that if we analysed the sites we could learn more about what life was like in 2008 and how these people went about buying cheap kitchen accessories and discount CDs.”

“These incredibly precise geometric patterns mean that the people who founded the Woolworths Empire must have used these store locations as a form of ‘landmark satnav’ to help hunters find their nearest source of cheap sweets that can be purchased in whatever mix they chose to pick. Well, that or the fact that in any sufficiently large set of random data it is possible to find meaningless patterns of any required accuracy.”

Thank you, Mr. Parker, for fighting the good fight.