A quick little news snippet from Science: The ESA's new satelitte, Planck, is due to launch on 5/14/09 and will take up the mantle of COBE and WMAP. However, in addition to just improving measurements of the Cosmic Microwave Background, Planck will also possibly prove inflationary theory.
The nuts-and-bolts of inflation say that, in the early early universe, an inversion of the Higgs field resulted in spacetime expanding at superluminal velocities and rapidly slowed down. This explains the flatness of space, the lack of magnetic monopoles, and perhaps the most importantly the uniform temperature of space. This could mean that parts of space no longer causally connected once were, and thus had time to reach a thermal equilibrium before expanding apart.
As a side-effect of inflationary theory, though, we expect to see B-mode polarization of the CMB (that is, polarization of the magnetic field). To quote the article:
But the prize quarry for Planck researchers is the B modes. These features are swirls in the CMB polarization mapped across the sky, and spotting them would essentially clinch the case for the mind-bending theory of inflation.
Although inflation fits the facts so far, researchers do not yet have direct proof that it occurred. The B modes would provide that. Current theory predicts that inflation should have generated gravitational waves and that those waves should have left lingering swirls in the polarization of the CMB.
The polarization may not be strong enough for Planck to detect, but with luck, they will be — and 45 years after the discovery of the CMB, and 30 years after the proposal of inflation, we might finally have an answer.
So, a quick read over the Science news this week led to an interesting news brief (DOI: 10.1126/science.324_578) about a paper that expanded on the 2007 claim that T. rex collagens were recovered (DOI: 10.1126/science.1165069 ; 2007 article DOI: 10.1126/science.1137614). [Edit: And my lagging on my Nature RSS also shows that Nature also had a very similar report (DOI: 10.1038/news.2009.422) ]
Composite picture of Brachylophosaurus. Color pictures from Wikipedia, reconstruction copyright Scott Hartman.
So, a refresher for those who don't remember: Back in 2007, Science published a paper that stated proteins from collagen fibers were recovered from a T. rex sample. While fascinating, the paper received much skepticism over the method, and this paper attempts to address that issue with a new genus and much more strictly controlled procedures.
By demineralizing the bone matrix of the fossil, and comparing it to a Struthio sample, the authors identified protein fragments with FESEM analysis and then checked for reactivity with antibodies to avian collagen I, ostrich whole bone extracts, and a specific epitope. The first two showed reactivity, but the last did not, indicated that this was either a novel epitope or simply not preserved. There were further antibody test against elastin, laminin, and hemoglobin (all associated with blood vessels), with were all also positive.
One of the more interesting points brought up in the article that wasn't really addressed in the news brief (though it certainly need much more research and a larger sample size) was that the antibodies (to ostrich bone extracts) used in the preparation to test binding to the proteins bound more strongly to the hadrosaur proteins than to G. gallus (chicken) proteins. If this result is consistent across more testing, it actually provides another reference point to the (uncontroversial) status of Paleognathene birds being basal to Neognathae.
Another big issue with the 2007 paper was the mass spectrometry. Its results were considered to be possibly contaminated with bacteria, and too close to noise level. In this experiment, the machine used was more sensitive, and analysed at two labs. The authors still found collagen peptide sequences.
When phylogenies were inferred from the collagen sequences, the results were consistent with inferences based on genetics and the fossil record. The sampled onithodirans ended up collapsing into a three-way polytomy, with Brachylophosaurus and Tyrannosaurus resolving as related to each other closely, but the relationship between the non-avian dinosauria and the sampled neornithines remained unresolved. This problem remained even with the removal of T. rex from the phylogeny, still leaving a three-way polytomy. The authors point out that there was, for obvious reasons, a fairly low resolution in Dinosauria, but B. canadensis still resolved as a derived archosaurian, more closely related to birds than to Alligator.
Now, its important to note that though this is incredibly cool, this is a far cry from Jurassic Park. The proteins recovered from the collagen fragments are incomplete, and it is highly unlikely that even an egg of an ostrich would provide a suitable oocyte for cloning. That said, however, this certainly has the promise of making paleontology gain a genetic basis for phylogenetics to complement the fossil record. Though, as this study showed, there's a way to go yet.
As an aside, does anyone think it'd be useful for me to put in a DOI search box on the right hand panel?
Schweitzer, M., Zheng, W., Organ, C., Avci, R., Suo, Z., Freimark, L., Lebleu, V., Duncan, M., Vander Heiden, M., Neveu, J., Lane, W., Cottrell, J., Horner, J., Cantley, L., Kalluri, R., & Asara, J. (2009). Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis Science, 324 (5927), 626-631 DOI: 10.1126/science.1165069
If you look at a (yikes! month old) Science "Letters", there an interesting, if brief, back-and-forth about sauropod neck posture between RS Seymour and PM Sander.
Up front, I'd like to say like Sander, I don't necessarily disagree with Seymour's conclusion; my own work (still undergoing revision that is halting its review process) strongly suggests that the necks were mostly held laterally, due to energetics and biomechanical concerns. However, I do take issue with the blanket scaling argument used on several points.
Ara ararauna (Blue and yellow macaw), Hawaii
First, it is important to note that the work done by Seymour is based on mammalian modeling. I have no comment as to whether it strengthens or weakens his argument this way; however, as a saurischian dinosaur, a bird would be a much more convincing model point. Second, their morphology is wildely divergent even from birds, the closest living species to them. The anology, even to birds, would be as problematic for me as the biomechanical study that based T. rex on Gallus gallus (chicken). Merely being a close relative does not ensure analogy; the musculature distribution, posture, and body shape in both cases are significantly different from the model animal. The results might very well be interesting, but they are not sure be relevant at all.
While I also have some issue with the "plug and chug" nature of the blood pressure calculations, those you can't really get around — though I'd at least like to know if it was based on mammals or birds.
Well, that's my 2 cents for now. More later.
Things have been rather full lately, so posting has been much more sporadic than I'd like — but to keep up the post frequency (IE, at least weekly), I introduce the Tuesday Tetrapod! At least a photo, and possibly a description of a tetrapod every Tuesday.
Today, let us start with Sceloporus magister, or the Desert Spiny Lizard:
Its scientific name comes from the bright ventral colors, most vivid in the genus.
Elizabeth the laptop has died suddenly of irreparable organ failure in her old age, as she approached her fourth birthday. Surgeons tried to find a solution, but a vital organ appeared to have experienced a memory parity error.
Liz was born in June 2005, a child with an adult's mind. Born with a form of CIPA, she was prone to overheating, but learned to mange this disability with education and practice. She broke her glasses several times, and as such, often had trouble reading when this happened. However, she had excellent artistic abilities, including some of the best artwork of her day and a great singing voice.
Elizabeth donated her organs to the less fortunate.
Now, this is pretty awesome — tying together biology and astronomy in one fell swoop. It turns out that the ten most common (of 20) amino acids are substantially more thermodynamically favorable to form. Now, that's certainly got to take a bit of wind out of creationist sails.
An amino acid. R represents a functional group. Shamelessly hotlinked from Wikipedia
Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these ten early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal.
The results here hinge on the fact that the ranked amino acid frequencies under various criterion correlate strongly (r=0.96) to ΔGsurf, where ΔG is the Gibbs free energy, which is defined as:
Source: Kittel & Kroemer 1980
Which is essentially the enthalpy of a system (loosely, the "thermodynamic potential energy") minus the fundamental entropy of a system
Source: Kittel & Kroemer 1980. g(N,U) is more commonly known as the "number of accessible microstates", and is sometimes denoted as W
multiplied by the fundamental temperature (the temperature in Kelvin times Boltzmann's Constant, 1.381 x 10-23 JK-1). In essense, the "sign" of this value (and its magnitude) denote how easy it is for them to spontaneously form. The lower the free energy, the less energy is needed to make a given event occur; thus, something with a negative free energy is spontaneous and releases energy upon its occurance, such as dissolving NaOH in water. Some other events take energy to occur, such as dissolving CaCl2 in water. Thus, in the first example, the beaker gets very hot, and in the second, it gets very cold. So, under the premise of the abiotic origin of life, one would expect the most "entrenched", or common, amino acids should be the easiest to produce. The results from the research support this conclusion:
|Group||Gsurf (kJ/mol)||Err||MW (Da)||Err||ATP cost||Err|
Table of values for early and late group amino acids. All errors +/-.
Clearly, the "early group" amino acids, the ones most common in organisms, and that are most simple to form abiotically, have a formation advantage in terms of energy, size, and spontaneity over other amino acids. This is further supported (with some caveats expressed in the paper) in that the amino acid distributions were a bit off for hyperthermophillic bacteria — i.e., the ones living around underwater hydrothermal vents. With the higher energy densities available, differences in amino acid synthesis costs may be a reason for different amino acid preferences in high-expression proteins (though the authors are quick to point out this may merely be an artifact of high temperature stability for proteins).
The remainder of the paper is also quite interesting, but requires a bit more knowledge of biochemistry than I'd like to assume for this blog. The authors touch on the diversity of amino acids, and why the observed diversity in nature is fewer than the maximum number.
Hmmm. A spurt of posting might be coming ...
Paul G. Higgs, Ralph E. Pudritz (2009). A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code Astrobiology DOI: arXiv:0904.0402v1
Yep, postless for a bit. Suffice it to say things have been hectic and suprisingly full. I have a list of things in my browser that auto open that I want to discuss, like stars in the Pleiades, sauropod neck position, still the Higgs post, and black holes.
However, until those get put up, I will just point you towards a researchblogging article by Grrlscientist (on Living the Scientific Life (Scientist, Interrupted)) about how birds read human eyes.
Also, via Badastronomy, I found out about the Florida Citizens for Science Stick Science competition. The idea is to make a stick-figure comic about a topic that is misunderstood in science (particularly evolution), and "correct the record". For my part, I've submitted the following:
Alternate: large PNG. Disclaimer: Yes, I know that cladograms aren't right for development of an organism. Its a parody. Put the point is you can replace a real transition with the tree development steps here and get the same response.
I amused myself with that one. That's it for now, though. For more random blog entries, Rachael has a cool one up on a caterpillar entering its chrysalis.
Alan: So, if you had to make a recommendation, Mac, PC, or Linux? Or do you find them to be equally (in)secure?
Charlie: I'll leave Linux out of the equation since I know my grandma couldn't run it. Between Mac and PC, I'd say that Macs are less secure for the reasons we've discussed here (lack of anti-exploitation technologies) but are more safe because there simply isn't much malware out there. For now, I'd still recommend Macs for typical users as the odds of something targeting them are so low that they might go years without seeing any malware, even though if an attacker cared to target them it would be easier for them.
Alan: Sure, the risk = threat x vulnerability x consequence concept. Macs have low threats but high vulnerability while Vista is the other way around. I recently switched to a Mac myself and wrote about it for Tom's Hardware (and had a lot of angry readers). Like you mentioned earlier, we want to support vendors with the most secure software, but it’s not easy to always figure out which software is the most secure and sometimes the real-world risk is lower with a vulnerable platform with fewer threats.
(Emphasis mine). There, definitive. Macs are less secure than PCs, just no one cares about them. Can the vehement Apple-fanboi crowd be quiet now? For the record — the Charlie here is the winner of Pwn2Own, a hacking contest with real-world software and operating systems. He cracked Leopard in under 2 minutes.
A little bit on Hesperonychus...
I managed to get a hold the paper on PNAS (DOI: 10.1073/pnas.0811664106), and I thought I'd flesh out what I thought was the most interesting report yesterday. First, a bit of clarification: I mentioned that it is the smallest, non-avian North American dinosaur yet found, but "small" is relative. Most people, thinking of carnivorous non-avian theropods, think of superpredators such as Allosaurus fragilis or tyrannosaurids.
Now, for many reasons, smaller specimens are not likely to be fossilized, despite being much more numerous than their superpredator bretheren. Being light of frame, they are more prone to scavanging, or direct physical damage to their remains. Thus, the fossil evidence becomes much more scant at lower mass ranges, and Hesperonychus is the first animal found in North America under 10 kg, under-massing Sauronitholestes langstoni.
Hesperonychus is further an interesting find in that it is a microraptorine dromaeosaurid (first one in North America), unlike other Dinosaur Park Formation dromaeosaurids found to date. The holotype pelvic girdle was discovered in 1982, but remained unidentified for a number of years (UALVP 48778, figure at right), but like many specimens, remained unstudied for a long time (25 years in this instance!). In addition to the holotype pelvis, Longrich et al. discovered a number of toes, including the typical sickle claw of basal dromaeosaurids. While superficially similar to the more infamous ones of Deinonychus, Utahraptor, and Velciraptor, the claw is less blade-like and resembles on close inspection (including on cross-section) that of microraptorines such as Rahonavis. The claw was quite small, only about a 1.5 cm long (projection, not along curve), but well-preserved. The precise cladistic placement of Hesperonychus is not particularly well defined, residing in a polytomy of various members of Microraptorinae. The number of phalaxes found (particularly phalanx II-3) suggest that there at least ten speciments in the TMP collections — when recognizing species by that element, for comparison, only 2 Dromaeosaurus specimens have been found, suggesting that Hesperonychus might have in fact been quite common in its day. This is especially true in light of how difficult preservation would have been!
It is finally worth noting that even though this is a tiny dinosaur at 1900 g, it outmasses the largest metatherian (early marsupial mammal) Eodelphis by 150% (600 g). Yep, mammals — still puny!
Longrich, N., & Currie, P. (2009). A microraptorine (Dinosauria-Dromaeosauridae) from the Late Cretaceous of North America Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0811664106
Please respect image copyright of the authors, and contact them for permission if you plan to use their images. Thanks!
Seems that the news has been an bit heavy on the fossil finds! How about a rundown.
Hesperonychus claw, hotlinked via National Geographic. The claw is on a Canadian penny.
First up is Hesperonychus ("western claw") — as yet, the smallest theropod found in North America. At the time of this writing, the PNAS paper isn't up yet, but in particular PhysOrg has a pretty good synopsis. As the name suggests (via a linguistic kinship to Deinonychus), Hesperonychus elizabethae is a diminuitive dromaeosaurid, approximately 2 kg and 50 cm tall "beating" Albertonykus borealis for title of "smallest North American non-avian dinosaur". It retains the trademark "sickle claw" of the dromaeosaurids, and the hip configuration was one of the primary diagnostic traits used to pin it to dromaeosauridae. The pelvis is also fused, suggesting that this was a mature adult. It's dated to about 75 million years ago (which the PhysOrg article accidentally writes as 45 million years ago, obviously in error at 20 MY after the K-T event).
Picture of the Svalbard excavation, from the New York Times.
The next big find announced today was of an unnamed, massive pliosaur found in the Svalbard region. I'm outright going to say I wish Kit had something to say about this, as I vaguely recall him mentioning this almost a year ago, and he knew some basics about it already. Never mind how he knows, considering it hasn't been published yet — the NYT article is already a pre-publishing press release.
At any rate, this guy was massive. This pliosaur had a skull measuring over 3m long, and the entire animal was probably longer than 15m at over 40 tonnes. Its "nickname" for now is "Predator X". Particularly novel about this find is that it might represent a new family of pliosaurs, which would be rather significant, paleontologically. Initial biomechanical work suggests its bit force would be 2-4 times that of T. rex and more than 10 times that of any extant animal. It was estimated to live about 150 MYA.
Figure 1 from Mud-trapped herd captures evidence of distinctive dinosaur sociality by Varricchio et al. 2008. (property of the authors)
Sinornithomimus dongi (Chinese bird mimic)is the next guy to hit to press. It has the slightly dubious distinction of being discovered when a large immature herd got stuck in a mud trap. It is siginificant in that the herd was apparently all juveniles, and in the number of animals found. With 25 individuals found (aged 1-7), this promises to make Sinornithomimus particularly well described. This was a bit of a late reporting on a December 2008 paper by Varricchio et al., which I've not had a chance to go over yet. I might update this with more detailed information once I get the chance.
I swear, I will post Higgs and the mouse post ...
The Cosmic Diary is not about the science of astronomy, but about what it is like to be an astronomer. Professionals will blog in text and images about their life, families, friends, hobbies and interests, as well as their work, latest research findings and the challenges they face. The bloggers represent a vibrant cross-section of working astronomers from around the world. They will write in many different languages and come from five continents. They will be asked to explain one particular aspect of their work to the public in more popular language. These "explanations" will be highlighted on the web and used as the basis for a book and documentary to be released during IYA2009 as the legacy of this project. [Source]
Yeah, I'm not even remotely official in this capacity. But, I did want some semi-official logo to stick on astronomy posts, and, helpfully, the IYA provided a source Adobe Illustrator file. Thus, I've appended the "Cosmic Blog" logo (with what I feel are better colors to boot) to the end of my astronomy posts, and will put them on all astronomy posts put up through 2009. Already, this blog is doing better than I'd hoped for in terms of updates — nothing like the Quantum Singularity blog (with all of 17 posts), and I'm keeping things a bit more informative. Not shabby!
In an amusing aside, the real Cosmic Diary site implemented an RSS fetching algorithm that's apparently less robust than my own — it took longer to load and threw an error instead of a graceful faliure.
Finally, is there any display problems with the Twitter feed on the right? It doesn't display right in Opera 10 (on my machine, anyway), but looks like it works on IE 8, Chrome 2, and FF 3. Safari, of course, being the poor Windows port it is, just spun its little pinwheel that covers up the "stop loading" button. Whoops.
The answer? You can't have a script closing tag in the document.write function, and to the best of my knowledge, you can't self-close a script tag. Thus, you need to hack it like so:
Small change, but amazingly nonobvious. Took me a long time to figure it out. And thus ends this rant.
Moral of the story? Stick with PHP and CSS. They're more standards-compliant, and way more intuitive. For example, they'd just use:
include("code.php"); // code.inc in some contexts ?>
@import "css_sheet.css"; /* This has different uses from <link> */
Much better, and much more intuitive!
Lets close this with something a bit less "ranty". It turns out that, finally, you can customize your logon background in Windows 7 without third party hackery — though you still need to do a few reg changes to pull it off.
In an effort to prove ever close to the ultimate answer, physicists and astronomers have been looking to probe gravity even deeper. The best results from orbiting pulsars agree with Einstein's theory of General Relativity to within 0.2%. Alternative models predict marginally, but measurably, different results with the most relativistic systems. The ultimate measure of relativistic gravity waves depend on orbital periods, eccentricity, and masses, so by seeking systems like these we can probe gravity even more deeply than we have already.
On the face of it, it may seem that 0.2% is good enough. 99.8% accurate will, in fact, get you to the Moon (in fact, that much error on your path amounts to a 1.74 km error in your landing site on a 384399 km trip). So why does it even matter? These alternative theories posit different fundamentals about the universe, including the necessity of dark matter and cosmic origin.
Now, the most relativistic pulsar system we know of is PSR J0737-3039 — it has an orbital period of 2.4 hours, and an orbital decay of its semimajor axis of 7 mm/yr due to gravitational radiation in the form of gravity waves. Being a pulsar, it is an incredibly accurate clock, and enables measurements of such fine precision to be made, that we need to (and can!) measure the effects of its movement through the galaxy on its orbital decay. So, Deller et al. (DOI: 10.1126/science.1167969) show that using the VLBI and about a decade of observation can smash the possible GR error (or disprove GR at these precisions!) down to 0.01%.
Think about it. We're measuring something located ~600 parsecs away (1800 light-years [Lyr], give or take), measuring its orbital decay to millimeters to narrow constraints on one of the two most accurate theories in science to being "only" 99.99% accurate, up from 99.8%. Astronomy (and science in general) — bloody amazing.
By the way — I provide many links to scientific papers, in large part for rigor's sake, but if any readers (how many readers do I have? Do I have any?) are having difficulty, I'll see what I can do about finding free alternatives, such as arXiv.org preprints.
Some quick updates on last week's Nature:
Scientists are coming up with a novel way to fight bacterial infections in light of antibiotic resistant strains of bacteria, such as MRSA: make viruses do the work for you. By engineering viruses to weaken bacteria, antibiotics become more effective. The trick is, actually not to kill the bacteria. If you kill the bacteria, selection works too strongly, and you have bacteria that become resistant to the viruses. Instead, by making the bacteria weaker, you need bacteria to survive a one-two punch: supression of lexA3 (renders bacteria unable to repair DNA as well) and drugs (particularly of the sort that damages DNA).
The catch? You need to engineer a bacteriophage that is very specific, down to strain. Unless entire cocktails can be manufactured, strain-specific identification is required.
Lets see if a bit on Higgs gets posted tonight, or if I'm lazy and go watch Dollhouse.