Collective Motion: A New Level of Design Found in Proteins
Evolution News & Views March 15, 2016 3:06 AM
A "previously unidentified mechanism for modulating protein affinity" has come to light. A team of scientists at the Max Planck Institute for Biochemical Chemistry, publishing in the Proceedings of the National Academy of Sciences, has identified new functional roles for collective motions within protein molecules. These motions, referred to as allostery, allow one end of the protein to affect a distant part through what is termed "allosteric communication."
Intermolecular interactions are one of the key mechanismsby which proteins mediate their biological functions. For many proteins, these interactions are enhanced or suppressed by allosteric networks that couple distant regions together. The mechanisms by which these networks function are just starting to be understood, and many of the important details have yet to be uncovered. In particular, the role of intrinsic protein motion and kinetics remains particularly poorly characterized. [Emphasis added.]
This is cutting-edge research. The team studied a common protein named ubiquitin which, as the name implies, is ubiquitous in the cell. It serves as a molecular "tag" on other molecules slated for degradation by the proteasome. As such, it needs to form connections with the proteasome and with a variety of other proteins. What they found is that distant parts of the molecule could affect binding affinity of other parts through motions transmitted throughout the entire molecule.
To determine how this collective motion influences bindingand other functions of ubiquitin (e.g., presence of different covalent linkages), we performed an extensive structural bioinformatics survey of known ubiquitin crystal structures. Because the peptide bond conformation was the most recognizable feature of the collective mode, we used its conformation as a "marker" for structural discrimination. Themost significant relationship we found was the universal association between the NH-in state and binding to the ubiquitin-specific protease (USP) family of deubiquitinases (Fig. S11). This association has been previously noted and issurprising because the peptide bond is at least 6.8 Å from any USP (Fig. 3A).
By comparing mutants with wild-type forms, the team found several kinds of motion that involve twisting, rocking and stretching. Mutations on a peptide bond between two specific amino acid residues, in particular, had a surprising effect, reducing binding affinity by a factor of 10 (or abolishing it altogether). This suggests low tolerance for mutation.
They found "strong allosteric coupling between opposite sides of the protein" in some cases. "Given the relative subtlety of the expansion and contraction" of allosteric interactions, they found it "surprising" again that two different states could produce large effects. It implies that ubiquitin and its ligand "appear to adapt their conformations mutually to establish a complementary binding interaction" for best fit at the appropriate times.
One mutant showed a two-fold weaker affinity for its particular USP. "Although this change may seem like a moderate effect," they note, "it isactually surprisingly large and highly significant when one considers that it is allosterically triggered by the simple rotation of a solvent-exposed peptide bond on a distal side of the protein."
These motions are so rapid -- on the order of microseconds -- they were not really considered significant until recently. Other motions they mention, like "pincer time" and "tumbling time," occur on different time scales, the former being quicker, the latter being much slower. This may suggest a kind of timing code for different functions.
Their conclusions reveal a significant new area of study: switch-controlled "allosteric communication" in protein molecules:
This study revealed an allosteric switch affecting protein-protein binding through collective protein motion at the microsecond time scale.... Whereas most known microsecond to millisecond time-scale motions involve excursions to excited, lowly populated states, this motion occurs between two ground state ensembles with nearly equal populations (NH-in and NHout). Strikingly, the peptide bond conformation is allosterically coupled through a diverse set of interactions that triggers contraction/ expansion of the entire domain. This type of global domain motion reveals apreviously unidentified mechanism for modulating protein affinity. The presence of this allosteric network suggeststhere may be heretofore undiscovered ways in which macromolecular assemblies and covalent linkages regulate ubiquitin binding. More broadly, this study demonstrates how relatively modest changes in hydrogen bond networks and the protein backbone can bring about distant changes in protein conformation and binding affinity.
We encounter, therefore, a whole new level of specificity in protein architecture. It's not the old picture of an active site surrounded by haphazard amino acid residues. Any change could affect the allosteric communication of the whole protein. Clearly, mutants were less able to take advantage of the benefits of collective motion.
How did an unguided process arrive at a molecular machine that not only grips its substrate and catalyzes a reaction efficiently, but moves with intrinsic twists and stretches to improve the grip? The design specs for proteins just shot up a notch, and along with them, the challenges to Darwinian evolution.
My Debate with Michael Ruse -- Evolution as a Rube Goldberg Machine
Cornelius Hunter March 17, 2016 3:32 AM
Editor's note: Evolution News is delighted to welcome back Dr. Hunter as a contributor. He is a Fellow with the Center for Science & Culture, Adjunct Professor at Biola University, and author of the award-winning Darwin's God: Evolution and the Problem of Evil. He blogs at Darwin's God
It was great to see Professor Michael Ruse again last week in Northern California for our debate on the question, "Is Evolution Compelling?" He was in good spirits as usual, and his jokes were much better than mine. But I had one big advantage over my erudite opponent: I was not defending the age-old idea that the world of life arose by chance. The main problem, as I explained at the outset, is that the scientific evidence contradicts unguided evolution. That is a very simple point, but it opens new worlds of thought.
I used my time to discuss a range of scientific evidence from biology. On that evidence, unguided evolution simply makes no sense. But I almost hesitate to show you my list simply because there is nothing special about it. One of the difficulties in explaining the problems with evolution to an audience is the plethora of examples from which to choose. I had a long list of fascinating biological designs that refute evolutionary thought. I like every one of them, because they all add a different angle on why evolution fails. But there are far too many to fit into an evening's presentation. I was changing my mind right up to the last day, but as difficult as it is, one must pare back the list to fit the time constraint.
I began with one of my favorites, micro RNA. I then discussed the failure of evolution's nested hierarchy. Later I had fun with echolocation and the DNA code, and I finished with directed adaptation. The obvious and unavoidable truth is that evolution is believed to be a fact not because of the science, but despite the science.
I also punctuated my scientific examples with some philosophy of science concerns. One of them is the problem of parsimony. I explained Occam's Razor, and how a sure sign of a failing theory is if it becomes overly complicated. The appeal of heliocentrism over geocentrism was not that of an improvement in accuracy, but in simplicity. Like heliocentrism, Copernicus' geocentrism had epicycles. So why make the move? Because Copernicus was able to use fewer epicycles. That is how important simplicity is in science.
Theory complexity is the enemy in science, and it would require volumes to explain all the details in today's theory of evolution. The reason why evolution is so complicated is that with each scientific failure, the theory is adjusted yet again. Today it resembles one of Rube Goldberg's wonderful machines.
For this theory, there is no ray of hope. I think I left the audience convinced that evolution is an utterly failed attempt. That's not because of any rhetorical skills on my part, but simply because I took the side of science. This isn't at all complicated. What is complicated is the question of why people believe in evolution to begin with. But that's another story.
That’s where the EHT comes in. Since the EHT first started taking data, it has been building its telescope roster, and with each new member, it gets closer to making the first true image of a black hole shadow.
The EHT is like an all-star team of telescopes: Most days, its millimeter-wave dishes run their own experiments independently, but for one or two weeks a year, they team up to become the EHT, taking new data and running tests during the brief window when astronomers can expect clear weather at sites from Hawaii to Europe to the South Pole.
“It sounds too good to be true that you just drop telescopes around the world and ‘poof!’ you have an Earth-sized telescope,” says Avery Broderick, a theoretical astrophysicist at University of Waterloo and the Perimeter Institute. And in a way, it is. The EHT doesn’t make pictures. Instead, it turns out a kind of mathematical cipher called a Fourier transform, which is like the graphic equalizer on your stereo: it divvies up the incoming signal, whether its an image of space or a piece of music, into the different frequencies that make it up and tells you how much power is stored in each frequency. So far, the EHT has only given astronomers a look at a few scattered pixels of the Fourier transform. When they compare those pixels to what they expect to see in the case of a true black hole, they find a good match. But the job is like trying to figure out whether you’re listening to Beethoven or the Beastie Boys based only on a few slivers of the graphic equalizer curve.
Now, the EHT is about to add a superstar player: the Atacama Large Millimeter Array, a telescope made up of 66 high-precision dishes sited 16,000 feet above sea level in Chile’s clear, dry Atacama desert. With ALMA on board, the EHT will finally be able to make the leap from fitting models to seeing a complete picture of the black hole’s shadow. EHT astronomers are now rounding up time at all of the telescopes so that they can take new data and assemble that first coveted image in 2017.
And if they don’t see what they expect? It could mean that the black hole isn’t really a black hole at all.
That would come as a relief to many theorists. Black holes are mothers of cosmic paradox, keeping physicists up at night with the puzzles they present: Do black holes really destroy information? Do they really contain infinitely dense points called singularities? Black holes are also the battlefield on which general relativity and quantum mechanics clash most dramatically. If it turns out that they don’t actually exist, some physicists might sleep a little better.
But if they’re not black holes, then what could they be? One possibility is that they are dark stars made up of bosons, subatomic particles that, unlike more familiar electrons and protons, obey strange rules that allow more than one of them to be in the same place at the same time. Boson stars are highly speculative—astronomers have never seen one, as far as they know—but theorists like Vitor Cardoso, a professor of physics at Técnico in Lisbon and a distinguished visiting researcher at Sapienza University of Rome, hypothesize that some or all of the objects we think are supermassive black holes could actually be boson stars in disguise.
Physicists classify particles into two different categories: fermions, which include protons, electrons, neutrons, and their components; and bosons, like photons (light particles), gluons, and Higgs particles. Every star that we’ve ever seen shining is dominated by fermions. But, Cardoso says, given a starting environment rich in bosons, bosons could “clump” together gravitationally to form stars, just as fermions do. The early universe might have had a high enough density of bosons for boson stars to form.
But not every boson is a suitable building block for a boson star. Gravity won’t hold together a clump of massless photons, for instance. Higgs particles are massive enough to be bound together by gravity, but they aren’t stable—they only exist for tiny fraction of a second before decaying away. Theorists have speculated about ways to stabilize Higgs particles, but Cardoso is more intrigued by the prospect that other, yet-undiscovered heavy bosons, like axions, could make up boson stars. In fact, some physicists hypothesize that massive bosons like these could be responsible for dark matter—meaning that boson stars wouldn’t just be a solution to the riddle of black holes, they could also tell us what, exactly, dark matter is.
Gravastars
Boson stars aren’t the only black hole doppelgänger that theorists have dreamed up. In 2001, researchers proposed an even more speculative oddity called a gravastar. In the gravastar model, as a would-be black hole collapses under its own weight, extreme gravity combines with quantum fluctuations that are constantly jiggling through space to create a bubble of exotic spacetime that halts the cave-in.
Theorists don’t really know what’s inside that bubble, which is both good and bad news for gravastars: Good news because it gives theorists the flexibility to revise the model as new observations come in, bad news because scientists are rightly skeptical of any model that can be patched up to match the data.
When the data does come in, physicists have a checklist of sorts that should help them know which of the three—black hole, boson star, or gravastar—they’re looking at. A gravastar should have a bright surface that’s distinguishable from the glowing ring predicted to loop around a black hole. Meanwhile, if the object at the center of the Milky Way is actually a boson star, Cardoso predicts, it will look more like a “normal” star. “Black holes are black all the way through,” Cardoso says. “If really the object is a boson star, then the luminous material can in principle pile up at its center. A bright spot should be detected right at the center of the object.”
A New View
Most physicists have placed their bets on Saggitarius A* and other candidates being black holes, though. Boson stars and gravastars already have a few strikes against them. First, when it comes to scientific credibility, black holes have a major head start. Astronomers have a solid understanding of the process by which black holes form and have direct evidence that other ultra-dense objects, like white dwarfs and neutron stars, which could merge to form black holes, really do exist. The alternatives are more speculative on every count.
Furthermore, Broderick says, astronomers have looked for the telltale signature of boson stars and gravastars at the center of the Milky Way—and haven’t found it. “The stuff raining down on the object will give up all its kinetic energy—all the gravitational binding energy tied up in the kinetic energy of its fall—resulting in a thermal bump in the spectrum,” Broderick says —that is, a signature spike in infrared emission. In 2009, astrophysicists reported that they had found no such bump coming from Sagittarius A*, and in 2015, they announced that it was missing from the nearby massive galaxy M87, too.
Cardoso doesn’t see this as a death-knell for the boson star model, though. “The field that makes up the boson star hardly interacts with matter,” he says. To ordinary matter, the surface of a boson star would feel like frothed milk. “We do not yet have a complete model of how these objects accrete luminous matter,” Cardoso says, “so I think that it’s fair to say that this is still an open question.” He is less optimistic about gravastars, which he describes as “artificial constructs” that are likely ruled out by the latest observations.
As the LIGO experiment gathers more data, theorists will get more opportunities to test their exotic hypotheses with gravitational waves. As two massive objects—say, a supermassive black hole and a star—spiral toward each other on the way toward a collision, gravitational waves carry away the energy of their motion. If one member of the spiraling pair is a black hole, the gravitational wave signal will cut off abruptly as the star passes through the black hole’s event horizon. “It gives rise to a very characteristic ringdown in the final stages of the inspiral,” Cardoso says. Because the alternative models have no such horizon, the gravitational wave signal would keep on reverberating.
Most astronomers believe that the waves LIGO detected were given off by the collision of two black holes, but Cardoso thinks that boson stars shouldn’t be ruled out just yet. “The data is, in principle, compatible with the two colliding objects being each a boson star,” he says. The end result, though, is probably a black hole “because it rings down very fast.”
LIGO is not designed to pick up signals at the frequency at which supermassive objects like Sagittarius A* are expected to “ring.” (LIGO is tuned to recognize gravitational waves from smaller black holes and dense stars like neutron stars.) But supermassive black holes and boson stars are in the sweet spot for the planned space-based gravitational wave telescope eLISA (the Evolved Laser Interferometer Space Antenna), slated for launch in 2034. “To confirm or rule out boson stars entirely, we need ‘louder’ observations,” Cardoso says. “EHT or eLISA are probably our best bet.”
Taking the Pulse
In the meantime, astronomers could measure waves from these extremely massive objects by precisely clocking the arrival times of radio pulses from a special class of dead stars called pulsars. If astronomers spot pulses arriving systematically off-beat, that could be a sign that the space they’ve been traveling across is being stretched and squeezed by gravitational waves. Three collaborations—NANOGrav in North America, the European Pulsar Timing Array, and the Parkes Pulsar Timing Array in Australia—are already scanning for these signals using radio telescopes scattered around the globe.
To Broderick, though, the big question isn’t which model will win out, it’s whether these new experiments can find a flaw in general relativity. “For 100 years, general relativity has been enormously successful, and there’s no hint of where it breaks,” he says. Yet general relativity and quantum mechanics, which appears equally shatterproof, are fundamentally incompatible. Somewhere, one or both must break down. But where? Boson stars and gravastars might not be the answer. Still, exploring these exotic possibilities forces physicists to ask the questions that might lead them to something even more profound.
“We expect that general relativity will pass the EHT’s tests with flying colors,” Broderick says. “But the great hope is that it won’t, that we’ll finally find the loose thread to pull on that will unravel the next great revolution in physics.”
Transhumanism is a materialistic religion that seeks to attain the comforts provided by faith through belief in technology as savior. One aspect of the movement is the quest for eternal life. Now, a hyper-rich Russian mogul hopes to live forever by uploading his personality to a robot. From the Telegraph story:
Web entrepreneur Dmitry Itskov is behind the "2045 Initiative", an ambitious experiment to bring about immortality within the next 30 years by creating a robot capable of storing human personalities.
The group of neuroscientists, robot builders and consciousness researchers say they can create an android that is capable of uploading someone's personality.
Mr Itskov, who has made a reported £1bn from his Moscow-based news publishing company, is the project's financial backer.
They believe that robots can store a person's thoughts and feelings because brains function in the same way as a computer.
Says Itskov, "Different scientists call it uploading or they call it mind transfer. I prefer to call it personality transfer."
Even if they could do this, however, so what? Whatever programming the robot was able to access, "Robot Itskov" still wouldn't be Itskov. Our beings are so much more than what we think and remember. For example, there are the subconscious, physical sensations caused by stimuli that trigger hormones and body chemicals, the experience of emotions, and for those who believe in such things, the spiritual element.
No matter how powerful the algorithms that governed an "immortality robot's" programming, it would exhibit -- at most -- a faux or mimicking of "personality." The person being mimicked -- the being the robot was supposed to have become -- would not be present.
Internal Constraints vs. External Pressures: The Revelations of Evo-Devo
Michael Denton March 14, 2016 3:29 AM
Editor's note: In his new book Evolution: Still a Theory in Crisis, Michael Denton not only updates the argument from his groundbreaking Evolution: A Theory in Crisis (1985) but also presents a powerful new critique of Darwinian evolution. This article is one in a series in which Dr. Denton summarizes some of the most important points of the new book. For the full story, get your copy of Evolution: Still a Theory in Crisis. For a limited time, you'll enjoy a 30 percent discount at CreateSpace by using the discount codeQBDHMYJH.
One of the major advances since the publication of Evolution: A Theory in Crisis has been the revolutionary increase in our understanding of development and especially the genetics of development, about which little was known in 1985. These advances have led to the emergence of a whole new field, nicknamed "evo-devo" (evolutionary developmental biology). At the heart of the new field has been the discovery that a limited set of highly conserved genes, gene circuits, and developmental mechanisms -- for example, Hox genes, signaling proteins such as "sonic hedgehog," chemical gradients, and gene regulatory networks -- are involved in the construction of the bodies of all bilaterally symmetric animals,1 all the morphological homologs, and indeed all higher organismic form. Sean Carroll has termed this set of conserved genes and developmental mechanisms the "toolkit."2
One now well-established finding of evo-devo was totally unexpected from Darwinian first principles. It is that what are referred to by evo-devo researchers as "constraints," or what might also be termed "internal causal factors," have played a far more important role in the origin of many of the homologs and Bauplans than was previously envisaged. Before evo-devo it was widely thought that internal factors played little or no role in shaping the course of evolution. But it is now increasingly obvious that internal causal factors have played a far more prominent role in the actualization of evolutionary innovations than cumulative selection.
One of the most fundamental of all evolutionary innovations occurred when some ancestral chordate switched its body plan from the design previously shared by all other animal groups (in which the nerve chord is in a ventral position and the heart and main blood vessel are placed dorsally) to a design that was the exact reverse (in which the nerve chord is placed dorsally and the heart placed ventrally), and that has remained invariant in all chordates ever since. The evidence for this dorsal-ventral inversion (D-V) was revealed when evo-devo studies showed that the signaling molecules that specify the back of an insect also specify the ventral side (the belly) of a vertebrate.3 Before evo-devo revealed that the same genes were involved in specifying the dorsal-ventral axis of chordates and non-chordates, no one took seriously Goeffroy's suggestion, made early in the 19th century, that all animals shared the same basic body plan.
Self-evidently, Darwinian scenarios must confront the obvious question as to whether this transition was gradual or sudden. On the one hand, it is very hard to imagine how gradual cumulative selection could carry out such a radical re-engineering of the basic body plan. What mystifying adaptive path can be proposed along which such a gradual transition might have occurred? On the other hand, if the change occurred suddenly in one massive macro-mutational saltation, then Darwinian causation is ruled out of court altogether.
In the case of this dramatic innovation, the revelations of evo-devo provide no support at all for the Darwinian notion that cumulative selection is the major causal engine of evolutionary transitions.
In taxa-defining homologs, it is self-evident that the emerging evo-devo picture provides no support whatsoever for the Darwinian claim that novelties came about during the course of evolution to serve a succession of functional ends. In this case, the structuralist inference that internal constraints and not cumulative selection played the key role in their actualization is difficult to refuse.
This example is not atypical. Evo-devo advances have revealed that in many, if not the great majority, of innovations in the history of life,internal causal factors have played a predominant role. Against all traditional expectations, Darwinian selection to serve adaptive ends could only have played, in most cases, a relatively peripheral causalrole. Before evo-devo, no one would have imagined that a vast amount of organic order arises from internal constraints and causal factors within organisms themselves and is not imposed by selection. What was heresy only three decades ago is now accepted doctrine.
References:
(1) Lewis I. Held, How the Snake Lost Its Legs: Curious Tales from the Frontier of Evo-Devo (New York: Cambridge University Press, 2014), Chapter 1.
(2) Sean Carroll, Endless Forms Most Beautiful, Chapter 3, see fig. 3.7.
(3) Held, How the Snake Lost Its Legs, Chapter 1; for alternate scenarios, see "Inversion (evolutionary biology)," Wikipedia, Wikipedia Foundation Inc., March 22, 2015 (accessed on August 19, 2015).
Witness this attack by University of Ottawa professor Stuart Chambers on the disability rights advocacy organization Not Dead Yet for its opposition to legalizing assisted suicide and euthanasia.
Chambers calls the organization's stance "unprincipled." Why? Because it distinguishes between the right to refuse life-sustaining medical treatment, which the group supports, and legalized euthanasia and assisted suicide, which it opposes implacably. From "Not Dead Yet: An Unprincipled Position Against Assisted Death":
Although the choices surrounding acts of commission and acts of omission could be similarly motivated by loss of autonomy, decrease in bodily function, or feelings of being a burden, Not Dead Yet only supports autonomous choice for passive treatment decisions (withholding or withdrawing life-sustaining treatment) that lead to premature death. To be consistent, Not Dead Yet should be lobbying for or against all end-of-life alternatives.
We've heard this same sophistry for decades. The truth is:
Withdrawing medical treatment may lead to death, but that isn't the intent. Indeed, the point is to stop an unwanted bodily intrusion, not to kill. As Paul Ramsey put it, that is treating the "patient as a person."
With the exception of a feeding tube, such deaths are uncertain. Sometimes -- if unexpectedly -- people live. For example, Karen Ann Quinlan lived about ten years after her respirator was removed.
Death is certain in euthanasia and assisted suicide.
When medical treatment is withdrawn or withheld on request, if it comes, the death is natural.
In euthanasia and assisted suicide, death is unnatural, e.g., a result of homicide or suicide.
In contrast to removing unwanted treatment, the intent of assisted suicide and euthanasia is to kill.
Not Dead Yet sees clearly that assisted suicide and euthanasia discriminate invidiously against people with disabilities because they treat them as a disposable caste whose lives are not worth saving if they become suicidal.
The vital distinction between "allowing to die" and "making dead" through homicidal or suicidal means was recognized 9-0 by the United States Supreme Court in the 1997 decision Vacco v. Quill:
[A] physician who withdraws, or honors a patient's refusal to begin, life sustaining medical treatment purposefully intends, or may so intend, only to respect his patient's wishes to cease doing useless and futile or degrading things to the patient when the patient no longer stands to benefit from them. ...
A doctor who assists a suicide, however, "must necessarily and indubitably, intend primarily that the patient be made dead." Similarly, a patient who commits suicide with a doctor's aid has the specific intent to end his or her own life, while a patient who refuses or discontinues treatment might not ...[and, indeed] may instead "fervently wish to live, but to do so free of unwanted medical technology, surgery, or drugs." [Citations omitted.]
In other words, the right to refuse unwanted medical treatment is not a "right to die" but a right to be free from unwanted bodily intrusions. So then were the nine Justices -- liberal and conservative -- who unanimously signed this decision "unprincipled?" Please.
We shouldn't be surprised by the attack on Not Dead Yet and the opposition of disability rights organizations to assisted suicide. They pierce the political and ethical sensibilities of those on the political Left. They appeal to secularist sensibilities and arguments. Most importantly, they are effective.
Advocates like Chambers would do well to learn the skill of three-dimensional thinking and making nuanced distinctions. It would help them understand cogent and sophisticated arguments against legalizing assisted suicide.
"Settled Science" and the Cambrian Explosion -- Geologists Weigh In
Evolution News & Views March 12, 2016 3:46 AM
Yesterday we considered the "settled science" explaining the Cambrian explosion in light of one of two new papers in the Geological Society of America Bulletin. In the second paper, also by geologists from Harvard (Smith et al., with Francis A. MacDonald participating in both papers), we travel to Mongolia.
Until the 1990s, large regions of outcrops that cross the Ediacaran-Cambrian boundary were inaccessible to Western scientists. The Harvard team performed an extensive mapping of the area, correlating the outcrops with each other, measuring carbon and oxygen ratios for thousands of samples, and integrating their findings with outcrops in other parts of the world. They begin by introducing the problem:
Since Charles Darwin's observation of the apparently rapid appearance of fossils in what is now known as Cambrian strata (Darwin, 1859), the Precambrian-Cambrian boundary has been widely regarded as one of the evolutionary pivot points in the history of life. Despite the persisting interest on this topic, the causes, triggers, and tempo of change remain controversial. Following the extinction of Ediacaran biota and the calcifying metazoan Cloudina, the early Cambrian (or Terreneuvian Series) encompasses an evolutionary interval characterized by increases in diversity and disparity(Marshall, 2006) that coincide with multiple carbon isotope excursions with amplitudes of <8 2006="" 2007="" 2010a="" 2011="" al.="" e.g.="" erwin="" et="" maloof="" nbsp="" porter="" span="" style="border: 0px; margin: 0px; outline: 0px; padding: 0px;" zhu="">over a geologically brief interval in Earth history
(Valentine, 2002).Most recently, Maloof et al. (2010a) suggested that the Cambrian fossil first appearances occurred in three discrete pulses associated with rapid reorganizations in the carbon cycle. To test this hypothesis and others about mechanistic links between environmental change and evolutionary milestones across the Ediacaran-Cambrian transition, it isnecessary to integrate records around the globe. However, previous global syntheses (e.g., Maloof et al., 2010a) have been limited to a small number of localities with large uncertainties in both local and global stratigraphic correlations and the lack of absolute ages directly linked to biostratigraphic and chemostratigraphic data, particularly with respect to critical data from Asia. Because the global data set is biased by just a few localities, refining local correlations and grounding them in regional geology arenecessary before an accurate global synthesis of fossil occurrence data can be constructed and interpreted. [Emphasis added.]
Similar problems were found in Mongolia as in the first paper: previous studies were flawed, and geochemical evidence did not correlate with fossil evidence. Once again, it's the local conditions that matter; "we suggest that this pattern is controlled largely by regional sedimentation and taphonomy [fossilization processes] rather than the rate of taxonomic origination," they say. ("Taxonomic origination" is a euphemism for "abrupt appearance of complex animals.")
One of their findings puts the squeeze on the evolutionary biologists. Their recalibration of the sequence puts the first appearance of small shelly fossils "hundreds of meters higher in the stratigraphy" than previously recorded, because earlier studies mistook an outcrop of phosphatic shale at one location with another fossil-bearing layer due to incorrect mapping. This compresses the time available for their evolution.
Reading these papers in detail, one gets the clear impression that geology is as much art as science. You can't just walk up to a wall of strata and read it like a book, much less use it like a Rosetta Stone to correlate with similar outcrops in other parts of the world. A great deal of interpretation is involved, even with empirical data like carbon and oxygen ratios. The authors use the word "interpret" frequently, even alleging that previous geologists misinterpreted things.
For example, one of the second paper's charts shows the small shelly fossils appearing in three pulses whose dates vary between Mongolia, Siberia, and China. Is this real, or an artifact of preservation?
We suggest that the apparent pulses of fossil first appearances are the result of intervals of nondeposition in the sections included in this compilation and do not represent global evolutionary patterns; FADs will not be found during periods in which sediment is not deposited. Charles Darwin(1859) suggested that the apparently rapid appearance of fossils found in Cambrian strata was a product of the incompleteness in the stratigraphic record -- at a smaller scale, this indeed may be the case.
If it "may" be the case on the smaller scale, it is clearly not the case on the large scale. Every Cambrian expert agrees that the fossil record is complete enough to consider the Cambrian explosion a major unsolved problem in biology.
Other complications appear in the paper:
Some of the strata are interpreted to be autochthonous (in their original position), and others are interpreted to be allochthonous (transported into place). There are flooding surfaces, intrusions, thrusts, bypass channels, subduction zones and unconformities. Much of the region is in a large basin that was infilled by sediments.
Some formations are "highly variable both in terms of thickness and lithology," with facies changes occurring over very short distances.
The authors infer periods of "depositional hiatus" in certain areas, one of them possibly up to 6-10 million years in length (this is to keep their correlations in sync).
They cannot account for the large "excursions" of carbon-isotope ratios (positive and negative) at certain levels. After considering various explanations, they say, "None of the hypotheses described above provides direct explanations for a mechanistic link between eustatic sea-level change and the isotopic variations." The measurements cannot, therefore, serve as unambiguous proxies for changes occurring in the global carbon cycle at different times. (This undercuts Maloof's 2010 hypothesis about three pulses of evolution tied to the carbon cycle and, instead, attributes the pulses to accidents of deposition.)
The dates of the carbon-isotope ratio excursions do not always match between different parts of the world, even though they are assumed to represent correlation "tie points." Mongolia has extra excursions, for instance, that do not appear in China or Siberia. "suggesting that the carbon cycle was oscillating even more rapidly than previously thought during the earliest Cambrian."
The first appearance of a trace fossil named Treptichnus pedum is considered diagnostic of the Ediacaran-Cambrian boundary around the world, but it appears at different dates in different locations. Because its appearance is strongly "lithofacies controlled" (dependent on the type of rock in the outcrop), "using T. pedum as a global chronostratigraphic marker has been problematic on most Cambrian paleocontinents, notably in Siberia, China, Mongolia, and Kazakhstan."
Some of the upper strata contain ultramafic minerals, representative of very high temperature volcanics that are atypical of the cooler mafic lavas observed today.
Some of the strata are stratified; others are not. Some contain conglomerates are even large boulders, representative of transport. Some of the conglomerates contain pebbles that are rounded and well sorted; others are angular and unsorted.
The strata contain chert, limestone, sandstone, siltstone, dolomite, ooids, and other minerals and structures that call for interpretation.
The Harvard team ties their carbon-isotope ratios to absolute ages from Morocco (a third of the way around the globe), but Morocco lacks the earliest Cambrian fossils. "Because there is no one section globally in which it is possible to integrate the ichnofossil record, body fossil record, carbon isotope chemostratigraphy, and absolute ages, the calibration of this evolutionarily important transition remains piecemeal, resulting in much uncertainty in determining rates of origination and geochemical change."
These complications make it likely that some future geologist will find flaws in this paper. If the science were settled, the Harvard team would not end with a call for "testable hypotheses that can be used to better constrain the relationships between biological and environmental change during this major transition in life." In other words, we geologists just see "first appearances" of complex creatures in a confusing bundle of rocks. Ask the biologists where they came from.
