“Darwin’s Extra Sense,” a new video produced by SFI External Professor Dan Rockmore and collaborators, explores the ways applied mathematics is opening doors to astonishing insights in the life sciences – from evolutionary biology to protein folding and brain science.
Watch “Darwin’s Extra Sense” here (45 minutes)
“The field of biology had taken awhile for quantitative efforts to enter it, and now it has been truly transformed,” says Rockmore, a professor of mathematics and computer science at Dartmouth College. He produced the film in collaboration with filmmakers Wendy Conquest and Bob Drake, with financial support from the National Science Foundation and SFI.
The film tells the story of how the mathematical articulation of heredity by Gregor Mendel and others saved Charles Darwin’s initially flawed theory of evolution theory.
Darwin is quoted on his inability to apply math rigorously to his research: “I deeply regretted that I did not proceed far enough at least to understand something of the great leading principles of mathematics, for men thus endowed seem to have an extra sense.”
redOrbit Staff & Wire Reports – Your Universe Online
A third, previously unidentified reason for the extreme elongation of snake and eel bodies has been discovered by a team of University of Zurich paleontologists who published their findings Monday in the journal Nature Communications.
The lengthy, slender and flexible bodies possessed by these creatures have evolved many times independently in the over 500 million years of vertebrate animal history, the study authors explained.
Scientists had previously reported the characteristic formed in one of two ways: either through the elongation of the individual vertebrate of the vertebral column, or through the development of additional vertebrae and associated muscle segments.
Now however, University of Zurich professor Marcelo Sánchez-Villagra and his colleagues have found a third mechanism of axial skeleton elongation.
[ Watch The Video: New Evolutionary Mechanism Found In Ancient Fish ]
Thanks to an exceptionally well-preserved 240 million year old fossil, the investigative team was able to learn that the vertebral column of the Saurichthys curionii (an extinct genus of ray-finned fish that lived in the Triassic period) has two vertebral arch per myomeric segment, not just one.
That structure caused an elongation of the creature’s body, while also giving it a longer appearance. Erin Maxwell, a post-doctoral researcher in Sánchez-Villagra’s group, said this particular evolutionary pattern for body elongation is new.
Previously, experts had only known about the increasing number of vertebrae and muscle segments and the elongation of the individual vertebrae as methods of body elongation.
“The fossils studied come from the Monte San Giorgio find in Ticino, which was declared a world heritage site by UNESCO in 2003,” the university said in a statement. “The researchers owe their findings to the fortunate circumstance that not only skeletal parts but also the tendons and tendon attachments surrounding the muscles of the primitive predatory fish had survived intact.”
According to Maxwell, the scientists were able to determine the flexibility and the swimming aptitude of theSaurichthys curionii because of the shape and arrangement of the fossilized tendons that were discovered.
She also explained the fish genus was clearly less flexible than modern eels and unable to swim long distances at high speeds like modern oceanic fish such as the tuna. Maxwell added the one-half meter long fossilized fish is comparable to the garfish or needlefish due to its appearance and lifestyle.
ROME—The controversy surrounding an unproven stem cell therapy in Italy may be drawing to a close. Italy’s Minister of Health Beatrice Lorenzin announced yesterday that Stamina, the Turin-based nonprofit foundation that developed the treatment, will not be allowed to test it on humans—at least not in Italy.
The so-called Stamina method is a treatment based on bone marrow stem cells that Stamina’s President Davide Vannoni claims can grow new neurons under specific conditions and hence cure several neurodegenerative diseases. However, while thousands of patients still support Stamina and its treatment, scientists believe the method has no scientific basis. In May, the government passed legislation providing €3 million for the treatment to undergo a clinical trial. But in July, Lorenzin ordered Stamina to release its scientific files concerning the treatment for scrutiny by a committee of scientific experts to assess if the method is safe and effective enough to enter human trials.
On 12 September, media reported that the experts had unanimously rejected the method, although the reasons behind the rejection were not released to the public. Now, a decree from the Ministry of Health states that the committee’s rejection was based on the following:
An “inadequate description of the method,” due to the lack of a description of the way cells should give birth to new neurons
On “the lack of quality controls on cells,” which makes the treatment hard to replicate, thus not guaranteeing safety and efficacy of the product
On the “potential risks involved, due to the lack of a clear plan of selection, screening and testing of the cells’ donors, resulting in the lack of exclusion of risks related to transmissible illnesses, such as HIV1 and HIV2.”
On other risks of serious sensitization. i.e. encephalomyelitis, as well as the risk of injection of bone material at the level of the nervous system
At a press conference yesterday, Lorenzin said: “I would have liked this story to have a different ending, but the Stamina method is not eligible for the trial." Stamina’s Vannoni toldScienceInsider that “the reasons for rejection are totally unfounded.”
The Italian stem cell community, which has opposed the method from the beginning, gave a sigh of relief. “After the scientific world stood up, the right decision has finally been taken,” says Michele De Luca, director of the Centre for Regenerative Medicine “Stefano Ferrari” in Modena, Italy. “The method does not exist: It has no scientific basis and could be dangerous.”
But the story does not end there. Dozens of patients are still receiving the Stamina method in a hospital in Brescia and a hundred others are on a waiting list following their appeal to Italian courts for the right to be treated by Stamina.
While it is now unlikely that a formal clinical trial will ever take place, it remains unclear whether patients will continue to receive the treatment. Lorenzin told ScienceInsider that the matter lies with the Minister of Justice, not Health. “I wonder how the judges will continue to impose access to treatment after the strong position taken by the Ministry of Health,” De Luca says.
Vannoni said that Stamina’s biologists are preparing to submit a paper to a peer-reviewed journal. He added that “the Minister of Health of an African country has already given the green light to human experiments for the treatment in that country.”
Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes. However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures.
Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level. Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution, although the extent to which sequence convergence between genera occurs across genomes is unknown.
A group of scientists recently analyzed genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus.
Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection.
University of Southern California professor and author of the book Planet Without Apes, Craig Stanford, says evangelicals who don't accept Darwinian evolution are being intellectually dishonest and dismissed evangelist Ray Comfort's recent film "Evolution vs. God" as nothing but "biblical porn."
Stanford, who appears in the 36-minute film, noted in a There Is No God podcast that Comfort, although a congenial guy, used dishonest tactics to lead four evolutionary scientists from leading universities to say what he wanted but cut them off in the film before they could get into a more comprehensive discussion of the topic.
He said the end result is a film that won't win any new converts and argued that people should ignore it.
"The best approach to people like him and the evangelical community that might be making films like this, in general, is to just ignore them because they're obviously preaching to the converted, they are not winning over any hearts and minds of anybody else who is not evangelical," said Stanford. "It's a bit of a silly approach that they have that's all about trying to validate their increasingly marginalized beliefs."
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"If you're not going to accept evolution I guess that's your civil right, but that means you're working on a fundamentally irrational and a kind of slightly crazy mindset," he continued.
The film, which has garnered more than three quarters of a million YouTube views and sold 180,000 DVDs, has reportedly irritated that atheist community.
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When the host of the interview suggested that Comfort lacked scientific understanding Stanford disagreed, but called him and other highly educated evangelicals intellectually dishonest.
"He seems like a bright guy and many evangelicals are doctors, lawyers and I think that they are bright people, but as you know you can be a very intelligent person but you can close off your knowledge in certain compartments," said Stanford.
"Basically those prejudices…I think they are intellectually dishonest," he noted.
"I know this will offend some people in the evangelical community who may be listening but that video to me is a great example of what I would call biblical porn. It's a whole set of images and words that are really intended mainly to titillate and excite evangelicals. There's actually no actual inquiry in that video into science vs. creationism," he said.
Arapaima, one of the world’s biggest freshwater fish and the largest freshwater fish of South America, is unique among fish – it can breathe air. The largest specimens can reach more than 2.5 m in length and weigh up to 200 kg.
Arapaima is torpedo-shaped with large scales and red markings. It is streamlined and sleek, with dorsal and anal fins set back near its tail.
The newly discovered arapaima, named Arapaima leptosoma, is the first new species described since 1847.
The specific name leptosoma derives from the Greek leptos (slender) and soma(body), in reference to the relatively slender body form of this species.
The new species is “distinguished from all other Arapaima by following three characters: dorsalmost lateralis sensory cavity on preopercle extremely slender; ventrolateral margin of head where third infraorbital meets anterior limb of preopercle strongly angled such that ventral surface of head is almost flat; and anterior third of dorsal-fin base covered with an enlarged, thickened sheath that hides anterior dorsal-fin rays when adpressed,” Prof Stewart described the new species in a paper published in the journal Copeia.
The only known specimen of Arapaima leptosoma was caught in 2001 near the confluence of the Solimões and Purus rivers in Amazonas State, Brazil.
“Collecting adult Arapaima involves considerable difficulties, both with logistics in the field and subsequent storage in museums,” Prof Stewart wrote in the paper.
“As this study demonstrates, however, collecting at least a few voucher specimens can greatly enhance our knowledge of these fascinating fishes. Many more are needed.”
“Arapaima have high economic, cultural, and scientific value, but their diversity has been overlooked for too long,” the scientist concluded.
Harvard Gazette The Muslim Brotherhood: Evolution of an Islamist Movement Harvard Gazette Wickham's new book, The Muslim Brotherhood: Evolution of an Islamist Movement, was published this year by Princeton University Press.
(Phys.org) —Ants and bees are surprisingly more genetically related to each other than they are to social wasps such as yellow jackets and paper wasps, a team of University of California, Davis, scientists has discovered. The groundbreaking research is available online and will be published Oct. 21 in the print version of the journal Current Biology.
At the end of August, a group of 140 palaeontologists from around the world gathered in Edinburgh to discuss their research, ranging from dinosaur feeding behaviour to pterosaur flight and the world’s largest bony fish – the latter being the outcome of research supported by Glasgow University and National Museums Scotland.
As part of the gathering – the 61st Symposium of Vertebrate Palaeontology and Comparative Anatomy – a special session was convened honouring the work of Stan Wood, one of Scotland’s most talented field palaeontologists.
Throughout his life, Stan showed that some of the world’s most important fossils could be found right here in Scotland. His excavations in Bearsden yielded remarkable 330 million-year-old sharks and at East Kirkton he discovered the famed “Lizzie”, one of the world’s oldest reptiles and now one of the treasures on display at the National Museum of Scotland. But now an even greater find is exciting the world’s palaeontological community.
There are a number of big questions in palaeontology, such as where and under what conditions did life first evolve; what caused the extinction of the dinosaurs; and what were the detailed steps in our own evolution? But one question has stood out for many years as a mystery: what did the earliest vertebrates (animals with backbones) look like, and under what conditions did they emerge on wto land?
Without those first steps on land, the whole array of vertebrate life that we see today, including ourselves, could not have evolved.
We know the transition to land occurred around 345-360 million years ago but, despite global searches for vertebrates from this period, only one or two fragmentary remains were discovered. Where were the fossils that would answer our questions?
This question puzzled a Harvard professor, Alfred Sherwood Romer, one of the most renowned vertebrate palaeontologists of recent times. He spent a part of his career looking for fossils from this time period, without success. The period came to be known as Romer’s Gap and it was even suggested that very few forms made it on to land during this interval.
To Stan, this merely represented a problem which he set out to resolve.
His characteristic vigour and determination eventually paid off with the discovery of a stunning cache of fossils from a site near Chirnside in the Borders.
Specimens found to date include plants, fish and amphibians, including an early amphibian which Stan christened “Ribbo” due to its prominent and well-preserved vertebrate structure. This has provided us with enough information to interpret what the creature may have looked like as it roamed the Tweed basin around 350 million years ago.
The importance of the find cannot be underestimated and it has formed the focus of a majorresearch initiative funded by the Natural Environment Research Council and Heritage Lottery Fund.
The fossils have been acquired by National Museums Scotland, which has teamed up with the British Geological Survey and the universities of Cambridge, Southampton and Leicester to not only study Stan’s finds, but also to continue the search for more fossils in the Tweed basin and to better understand Scotland’s environment at the time.
To date, a key part of the study has involved the drilling of a 500-metre borehole. This will form the anchor stone for the team to date all of the fossil finds and hopefully piece together the story of how vertebrates colonized land.
This is a significant part of our natural heritage and the research team has made a strong commitment to bring the science to the widest possible audience.
Delegates at the symposium heard how the careers of professors Mike Coates from the University of Chicago and John Long from Flinders University were shaped and influenced by Stan’s discoveries and encouragement.
Details of how Romer’s Gap is now being filled featured strongly, with Professor Jenny Clack and Dr Tim Smithson of the University of Cambridge, providing first insights into these tantalising new fossils.
Stan sadly died last year, but his legacy lives on, in some respects echoing that of Edinburgh’s James Hutton, the father of modern geology, who established the importance of Scotland as a place for students of the earth sciences.
There is no doubt that Stan’s discoveries will continue to shape the careers of such students for generations to come.
• Dr Nick Fraser is Keeper of Natural Sciences, National Museums of Scotland www.nms.ac.uk
Biology student uses articulation program to fast-track to medical school UMSL Daily (blog) Weaver, a junior biology major, is benefiting from one of a series of agreements UMSL has recently put into place with other universities to ramp up...
CSET Biology/Life Science Exam Secrets Study Guide: CSET Test Review for the California Subject Examinations for Teachers [CSET Exam Secrets Test Prep Team] on Amazon.com. *FREE* super saver shipping on qualifying offers.
The newly emerged Middle East respiratory syndrome coronavirus (MERS-CoV) that first appeared in Saudi Arabia during the summer of 2012 has to date (20th September 2013) caused 58 human deaths. MERS-CoV utilizes the dipeptidyl peptidase 4 (DPP4) host cell receptor, and analysis of the long-term interaction between virus and receptor provides key information on the evolutionary events that lead to the viral emergence.
Findings We show that bat DPP4 genes have been subject to significant adaptive evolution, suggestive of a long-term arms-race between bats and MERS related CoVs. In particular, we identify three positively selected residues in DPP4 that directly interact with the viral surface glycoprotein.
Our study suggests that the evolutionary lineage leading to MERS-CoV may have circulated in bats for a substantial time period.
Posted by Martin S Pribble on October 11, 2013 in Featured, Thoughts
Of all the faith based beliefs, none can be more destructive than that of dominionism. Dominionism is the belief that the earth was put here, by God, for the exclusive use of humanity, and for humanity to exploit right up until the day of judgement. To those of us that don’t believe, this seems rather an innocuous belief, and one that seemingly we could choose to ignore, along with the tale s of Mohammed flying to heaven on the back of a winged horse, or the story of a talking snake, but unfortunately this belief brings with it a curse for all the people of earth. And it brings with it some very powerful corporate allies, ones that have a vested interest in the continued use and consumption of the earth’s resources. This is a very important aspect of the story, but first, let’s look at dominionism and what the adherents to this belief claim.
Dominionism, and “dominion theology” derives its roots from the opening chapter of the Old Testament, where in Genesis 1:27-30 it states (emphasis mine:
“27 So God created mankind in his own image, in the image of God he created them; male and female he created them.
28 God blessed them and said to them, “Be fruitful and increase in number; fill the earth and subdue it. Rule over the fish in the sea and the birds in the sky and over every living creature that moves on the ground.”
29 Then God said, “I give you every seed-bearing plant on the face of the whole earth and every tree that has fruit with seed in it. They will be yours for food. 30 And to all the beasts of the earth and all the birds in the sky and all the creatures that move along the ground—everything that has the breath of life in it—I give every green plant for food.” And it was so.
In these passages is the basis for all of dominionist theology, the idea that a god blessed the humans of earth with the bountiful boon of the earth’s wealth, and literally gives permission for the use of all the earth’s resources. It can be seen by some as a prime directive, a mandate to “fill the earth” with people, “and subdue it” by the hand of man. The language of this piece should give you some clue as to why this idea is so harmful.
The word “subdue” is a synonym for “defeat“, and immediately sets up the earth, not only as a place that we own, but an enemy that needs to be subjugated and controlled. When you see the earth as the enemy, then you’re setting the scene of the most epic battle in the earth’s history; Not a battle between god and Satan, as in the biblical prophecies, but a battle between humankind and the very planet that sustains it.
Many see these passages as a call for humans to look after and “steward” the earth, as in the case of The Cornwall Alliance, who claim to be “evangelical stewards”, preaching these words in a passive manner. In this sense, we have become so powerful on this earth with our tools of destruction that I see no alternative than to become caretakers of the fragile planet we inhabit, but as we shall see, The Cornwall Alliance’s standpoint is a dominionist one, wrapped up in passive language, where the earth cannot be damaged by the hands of humans, and if it is, then it is god’s will that we do just that. In a dominionist standpoint, these words are translated to say that humanity should not only rule over the earth, but also that Christian theologists should have a hand in the civil and political aspects of society, and thereby removing the idea of a separation of church and state.
Dominion theology stands on the grounds of several assumptions, and builds actively toward a single outcome.
The first assumption is that the Bible is literally the holy word and law of a creator god. This law is infallible, and is to be taken literally. Therefore the stories of the seven days of creation, Adam and Eve and “the fall”, Moses, Noah and the Israelites , are all presented in the bible literally as fact. The words of the bible are seen as a literal text of our human histories, and are a literal law-book of how we should conduct ourselves here on earth.
The second assumption is that, if the apparent law of god is followed to the letter, then the faithful will attain a seat in heaven after they die, right next to Jesus on his throne. Again this is to be take literally, for they truly believe that not only heaven exists, but that they will go to this magical place when their heart stops beating and they are lain to rest.
The third assumption is, if the earth was created for humankind by god, that surely anything build by a perfect being must, in itself, be perfect. Therefore we have no need to sustain the earth and its resources because they are all here for us to use as we see fit. This brings me to the foregone conclusion as preached by dominionist theology.
The inevitable outcome from this line of faith is that it doesn’t matter what we do to the earth, because as it states in the bible, there will come a time when the heavens open up and all the righteous and faithful will be drawn up into heaven, literally. The rest of humankind will be left behind on earth for Satan and his minions to do with as he pleases, eventually being drawn down into hell to suffer for eternity alongside Christopher Hitchens. This is the apparently inevitable outcome of this kind of biblical literalism, and points out precisely why dominionist theology is so dangerous.
The real danger in dominionism lies in the ties the dominionists have with government and big business, and it only takes a little scratching of the surface to see that many of those preaching the use and abuse of the earth’s resources are backed by those companies who stand to lose the most under a more sustainable human presence. The Cornwall Alliance, as mentioned above, are given donations from Exxon Mobil, enough money to keep the likes of Calvin Beisner and his “Green Dragon” mob afloat. This article from ThinkProgress.com goes into detail about these “contributions” from Exxon Mobil. This is the kind of conspiracy that’s hard to refute, when the public records show that this is the case.
Why would Exxon Mobil, and other petrochemical companies be interested in the preaching of biblical literalism? Because, they sell the very products that are causing the greatest harm to the environment, from plastics and other petrochemicals, to gas, oil and coal. The dominionist standpoint is one where the world is there to be used, and the petrochemical companies, whether religious or not, are doing their best to see that we do use all we can. The increasing trend in gas and oil extraction to go to greater lengths to procure them, such as fracking and tar sands extraction, shows how desperate times have become for these mega-corps, and they are determined to see that we buy their product at whatever the cost to the planet.
While I understand that much of the way the world is run today depends upon our insatiable greed for oil, gas and coal, it’s the short-term thinking of the consumerist culture that is the most dangerous to us. It will take a great change in the way we do things to sustain the planet’s 7 billion-plus people, and even more resources will be needed by 2050, where the world is expected to be host to up to 9 billion people. But according to the dominionists, this is not a problem, because the end-days are already upon us.
It seems that most of the dominionist rhetoric and action is surfacing in the USA, and it would seem that it’s tied directly into a sense of “American exceptionalism“, the idea that the USA is far superior to the rest of the world in all ways, because the American people have been chosen by god as the earth’s representatives. The idea of exceptionalism seems to walk hand-in-hand with the ideals of the dominionists, many of whom see America as the prophesied “final battle ground”, where god and Satan will play out the apocalyptic battle over souls. This is alarming, and while we could easily be forgiven for thinking that dominionism is just a small group of extremists, it seems the tentacles of dominionism reach deep into the ranks of the American government.
Dominionism is incredibly tenacious also. As Chrys Stevenson wrote on the ABC’s “Religion and Ethics” website:
In order to achieve their aim, dominionists plan to infiltrate, influence and eventually take over seven key spheres of society: business, government (including the military and the law), media, arts and entertainment, education, the family and religion.
If the ideals of the dominionists were truly of “stewardship”, we could forgive them their delusions about god and Jesus and the apocalypse. To practice true stewardship, helping and guiding the world toward a cleaner, more sustainable future, would actually be a boon to society, one that could be embraced by the religious and the secular alike. However their preoccupation with the “end times” means their focus is skewed, and their willingness to get on-board with big business to sell their ideal of “salvation” comes to the fore.
This is where religion becomes very dangerous indeed. The religious backing and promotion of the continued dependence upon fossil fuels, something we now know without a doubt is hurting the earth’s environment, is on par with treason to the human race, and we should not stand idly by and let the dominionist vision of the end-days come to fruition.
Prinsepia utilis Royle is a wild woody oil species of Rosaceae that yields edible oil which has been proved to possess particular benefits for human health and medical therapy. However, the lack of bred varieties has largely impeded exploiting immense potentials for high quality of its seed oil. It is urgently needed to enlarge the knowledge of genetic basis of the species and develop genetic markers to enhance modern breeding programs. Results
Here we reported the complete chloroplast (cp) genome of 156,328 bp. Comparative cp sequence analyses of P. utilis along with other four Rosaceae species resulted in similar genome structures, gene orders, and gene contents. Contraction/expansion of inverted repeat regions (IRs) explained part of the length variation in the Rosaceae cp genomes. Genome sequence alignments revealed that nucleotide diversity was associated with AT content, and large single copy regions (LSC) and small single copy regions (SSC) harbored higher sequence variations in both coding and non-coding regions than IRs. Simple sequence repeats (SSRs) were detected in the P. utilis and compared with those of the other fourRosaceae cp genomes. Almost all the SSR loci were composed of A or T, therefore it might contribute to the A-T richness of cp genomes and be associated with AT biased sequence variation. Among all the protein-coding genes, ycf1 showed the highest sequence divergence, indicating that it could accomplish the discrimination of species within Rosaceae as well as within angiosperms better than other genes. Conclusions
With the addition of this new sequenced cp genome, high nucleotide substitution rate and abundant deletions/insertions were observed, suggesting a greater genomic dynamics than previously explored inRosaceae. The availability of the complete cp genome of P. utilis will provide chloroplast markers and genetic information to better enhance the conservation and utilization of this woody oil plant.
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