Today in the News (June 26, 2009)

Evolution

Here's some interesting news on the subject of genetics from Science Daily (June 26, 2009):

Gene Evolution Process Discovered

One of the mechanisms governing how our physical features and behavioural traits have evolved over centuries has been discovered by researchers at the University of Leeds.

Darwin proposed that such traits are passed from a parent to their offspring, with natural selection favouring those that give the greatest advantage for survival, but did not have a scientific explanation for this process.

In new research the Leeds team reports that a protein known as REST plays a central role in switching specific genes on and off, thereby determining how specific traits develop in offspring.

The study shows that REST controls the process by which proteins are made, following the instructions encoded in genes. It also reveals that while REST regulates a core set of genes in all vertebrates, it has also evolved to work with a greater number of genes specific to mammals, in particular in the brain – potentially playing a leading role in the evolution of our intelligence.

Says lead researcher Dr Ian Wood of the University's Faculty of Biological Sciences: "This is the first study of the human genome to look at REST in such detail and compare the specific genes it regulates in different species. We've found that it works by binding to specific genetic sequences and repressing or enhancing the expression of genes associated with these sequences.

"Scientists have believed for many years that differences in the way genes are expressed into functional proteins is what differentiates one species from another and drives evolutionary change – but no-one has been able to prove it until now."

[...]

Click on the above link to continue.

Vaccines

Here's another interesting news item from Science Daily (June 26, 2009); this time on the subject of vaccines:

New Images May Improve Vaccine Design For Deadly Rotavirus

Howard Hughes Medical Institute researchers are reporting the first detailed molecular snapshots of a deadly gastrointestinal virus as it is caught in the grasp of an immune system molecule with the capacity to destroy it. The images could help scientists design a more effective vaccine against rotavirus, a lethal infection that kills more than 500,000 children worldwide each year. The discovery is timely.

Last week the World Health Organization recommended that rotavirus vaccination be included in all national immunization programs worldwide. Virtually every child in the world becomes infected with rotaviruses before developing natural immunity. But each year an estimated two million children are hospitalized because rotavirus infection results in severe dehydration caused by diarrhea and vomiting.

Both natural and vaccine-induced immunity occur only after the immune system has "seen" the virus and generates neutralizing antibodies. These soldiers of the immune system seek out and attach to rotavirus particles, rendering them unable to infect cells.

In the new experiments, Howard Hughes Medical Institute (HHMI) researchers have mapped the structure of an antiviral antibody clamped onto a protein called VP7 that stipples the surface of rotavirus. The structural map reveals intimate new details about how the antibody interferes with VP7, a protein that helps the virus infect cells. The information may be useful in designing a new generation of rotavirus vaccines that could be easier to store and administer than current vaccines, said the researchers.

[...]

Click on the above link to continue.

Today in the News (June 23, 2009)

Evolution

News can be like buses: you wait bloody ages for one to arrive, and then three four arrive at once! So, here are three four news items from Science Daily (June 23, 2009):

Social Competition May Be Reason For Bigger Brain

For the past 2 million years, the size of the human brain has tripled, growing much faster than other mammals. Examining the reasons for human brain expansion, University of Missouri researchers studied three common hypotheses for brain growth: climate change, ecological demands and social competition. The team found that social competition is the major cause of increased cranial capacity.

To test the three hypotheses, MU researchers collected data from 153 hominid (humans and our ancestors) skulls from the past 2 million years. Examining the locations and global climate changes at the time the fossil was dated, the number of parasites in the region and estimated population density in the areas where the skulls were found, the researchers discovered that population density had the biggest effect on skull size and thus cranial capacity.

"Our findings suggest brain size increases the most in areas with larger populations and this almost certainly increased the intensity of social competition," said David Geary, Curator's Professor and Thomas Jefferson Professor of Psychosocial Sciences in the MU College of Arts and Science. "When humans had to compete for necessities and social status, which allowed better access to these necessities, bigger brains provided an advantage."

The researchers also found some credibility to the climate-change hypothesis, which assumes that global climate change and migrations away from the equator resulted in humans becoming better at coping with climate change. But the importance of coping with climate was much smaller than the importance of coping with other people.

"Brains are metabolically expensive, meaning they take lots of time and energy to develop and maintain, making it so important to understand why our brains continued to evolve faster than other animals," said Drew Bailey, MU graduate student and co-author of the study. "Our research tells us that competition, whether healthy or not, sets the stage for brain evolution."

More from ScienceDaily (June 23, 2009):

54-million-year-old Skull Reveals Early Evolution Of Primate Brains

Researchers at the University of Florida and the University of Winnipeg have developed the first detailed images of a primitive primate brain, unexpectedly revealing that cousins of our earliest ancestors relied on smell more than sight.

The analysis of a well-preserved skull from 54 million years ago contradicts some common assumptions about brain structure and evolution in the first primates. The study also narrows the possibilities for what caused primates to evolve larger brain sizes. The study is scheduled to appear online the week of June 22 in the Proceedings of the National Academy of Sciences.

The skull belongs to a group of primitive primates known as Plesiadapiforms, which evolved in the 10 million years between the extinction of the dinosaurs and the first traceable ancestors of modern primates. The 1.5-inch-long skull was found fully intact, allowing researchers to make the first virtual mold of a primitive primate brain. [...]

Click on the above link to continue.

Even more from ScienceDaily (June 23, 2009):

How Big A Role Does Chance Play In The History Of Life?

If the broad evolutionary diversification of a group of organisms were repeated by a few species in a single genus tens of millions of years after the group's initial diversification, what would that say about the roles of contingency, constraint, and adaptation?

As Darwin observed, natural selection leading to adaptation of individuals and populations is occurring gradually and all the time. But over very long spans of time, the major channels of genetic organization, organism form, and the different ways organisms develop arose as outcomes of history-dependent variation that is now channeled, or constrained, within different groups of organisms.

For example, most cats look like cats, develop like cats, but have a fossil record that begins from less than cat-like ancestors. So do snails, and crabs, and so on. But what if the broad evolutionary diversification of one of these groups were repeated by a few species in a single genus tens of millions of years after that initial diversification? What would that say about the roles of contingency, constraint, and adaptation? In other words, how big is the role of chance in the history of life?

An international team of researchers including Field Museum curator Scott Lidgard, PhD, has discovered a group of closely related living species that independently repeated the different step-like changes that occurred in the major diversification of their kind during the Cretaceous Period, roughly 100 to 90 million years ago. But this group of species arose 80 million years later! [...]

Click on the above link to continue.

Autism

The subject of autism is usually the department of my brother-in-arms, Larian LeQuella, because of his own personal interest; however, since he is pre-occupied with more important matters, I will fill-in for him. So, I stumbled upon this article in Science Daily (June 23, 2009) that may be of interest to concerned parties:

ADHD Genes Found, Known To Play Roles In Neurodevelopment

Pediatric researchers have identified hundreds of gene variations that occur more frequently in children with attention-deficit hyperactivity disorder (ADHD) than in children without ADHD. Many of those genes were already known to be important for learning, behavior, brain function and neurodevelopment, but had not been previously associated with ADHD.

"Because the gene alterations we found are involved in the development of the nervous system, they may eventually guide researchers to better targets in designing early intervention for children with ADHD," said lead author Josephine Elia, M.D., a psychiatrist and ADHD expert at The Children's Hospital of Philadelphia.

Unlike changes to single DNA bases, called SNPs or "snips," the alterations examined in the current study are broader changes in structure. Called copy number variations (CNVs), they are missing or repeated stretches of DNA. CNVs have recently been found to play significant roles in many diseases, including autism [Editor: my emphasis] and schizophrenia. Everyone has CNVs in their DNA, but not all of the variations occur in locations that affect the function of a gene. The current study is the first to investigate the role of CNVs in ADHD.

Individually, each CNV may be rare, but taken together, a combination of changes in crucial regions may interact to raise an individual's risk for a specific disease. "When we began this study in 2003, we expected to find a handful of genes that predispose a child to ADHD," said study co-leader Peter S. White, Ph.D., a molecular geneticist and director of the Center for Biomedical Informatics at Children's Hospital. "Instead, there may be hundreds of genes involved, only some of which are changed in each person. But if those genes act on similar pathways, you may end up with a similar result—ADHD. This may also help to explain why children with ADHD often present clinically with slightly different symptoms." [...]

Click on the link to continue.

Today in the News (19 Jun 09)

Today I have a couple of much longer and more relevant articles for you.

Vaccines/Autism:
Somehow I missed this article in the Skeptic eNewsletter. It's a great rundown. Here is a brief excerpt:

During a question and answer session after a talk I recently gave, I was asked for my opinion about the vaccine/autism controversy. That was easy: my opinion is that there is no controversy. The evidence is in. The scientific community has reached a clear consensus that vaccines don’t cause autism. There is no controversy.

There is, however, a manufactroversy — a manufactured controversy — created by junk science, dishonest researchers, professional misconduct, outright fraud, lies, misrepresentations, irresponsible reporting, unfortunate media publicity, poor judgment, celebrities who think they are wiser than the whole of medical science, and a few maverick doctors who ought to know better. Thousands of parents have been frightened into rejecting or delaying immunizations for their children. The immunization rate has dropped, resulting in the return of endemic measles in the U.K. and various outbreaks of vaccine-preventable diseases in the U.S. children have died. Herd immunity has been lost. The public health consequences are serious and are likely to get worse before they get better — a load of unscientific nonsense has put us all at risk.

And it would probably be a good idea to read the article that preceded this one as well. Between these two articles, I still can't understand how people buy into the lies and deceit of the anti-vax pro-disease brigade, but they do. We still have a lot of work to do!

Evolution:
For today, I wanted to have a more lighthearted bit of news. The Florida Citizens for Science sponsored a contest where you could draw a stick figure comic talking about some classic mistakes people make in thinking about science. My wife and I both entered the contest, and we both placed in the top ten (although I hear her entry beat mine, how humiliating!). Please head over to the page and check out the comics, I think some are indeed much more worthy than mine and I am glad they beat me.

Okay, that's all I have for today. Hopefully other contributors have things for thei weekend. Also, I may be quiet on Monday and Tuesday due to a job interview that I will need to travel for. And as always, we are still looking for contributors to this site. If you have interest in helping this site out, please get with us.

Today in the News (18 Jun 09)

Vaccines:
Considering that "a malaria vaccines was considered laughable five to seven years ago", I was encouraged by a sort of behind the scenes look at the research. Considering how many people die from malaria, as well as the ever expanding range of mosquito habitats.

In the effort to develop an HIV vaccines, it helps to understand the evolution of the virus. Again, it is really quite amazing to consider how inter-related so many fields are!

Autism:
Again, to dismiss the idea that the Chinese don't have a word for autism (they do), here is an article about some difficulties Chinese parents are facing. Yes, they do have a word for it, but it's not as readily discussed there as it is here.

Scientists at UC Davis have discovered a link between a neuron protein and autism. This was particularly interesting again, because now it seems that once again the link is more genetic.

Evolution:
Maybe an effort to make evolution more understandable, looking at the evolution trees of species is a great tool. The University of Texas has made a great computer program that could revolutionize this tool.

And just because science may have a fit or disagreement about a specific item within a theory does not invalidate the entire theory. That's like saying all automobiles should be discarded on account of an argument on the brands of spark plugs. So I enjoyed this quick entry about the "Red Ape" theory. More a history lesson as well as a science lesson.

Today in the News (17 Jun 09)

Vaccines:
Here is an interview/book review where they discuss the eradication of Smallpox. Can you imagine if this effort had been fighting today's anti-vax pro-disease movement? Would countless deaths and the opportunity to make something just a distant memory be enough to get them to understand that in science, there is always a weighing of risk versus benefits? Or are they so self centered and craving attention, that they would rather put millions at risk?

Here is an OpEd piece discussing how emotions are horrible guides when it comes to the scientific. Particularly addressing the non-existent link between autism and vaccines. Well worth the read.

Autism:
One handicap of the autism spectrum disorders is being able to put names and faces together. That is why I found this article interesting. Especially the implications to the many other aspects of how people deal with others as well as objects even.

While the generally accepted view of autism is as a handicap, keep in mind that quite often it manifests as a narrow focus, or even a hyper focus. This has manifested in some research regarding problem solving. The key take away though is that there are still so many things that we just don't understand about autism and how it truly affects the individual.

Evolution:
First of all, I wish that there was a better way to bring pay journals to the public. In my daily search on articles, I ran into some very interesting stories that not only highlighted the interconnectedness of genetics and evolution, but also gave a great understanding to the complexity and wonder of it! Sadly, the journals are probably beyond the reach of most citizens.

Again, while abiogenesis isnt evolution, just the starting point, I found this article particularly fun and entertaining to read. I must say that it is pretty speculative, but if the speculations ahve any data to support them, they are worthy of persuit. However, should the data not support the speculation, then the theory needs to be shelved (you know, that stuff that science does).

In tracking the amazing evolution of humans, the University of Leeds has tracked down some interesting information on how our behavioural and physical traits evolved. I am particularly interested in where else this REST protien shows up.

Today (16 Jun 09)

Today was a good day overall for the skeptical movement. So instead of covering the same three topics that I type up on most days, I am going to repost a blog entry from Dr. Phil Plait (the guy that inspired this web page and who is also the president of the JREF). Enjoy the good news, and remember that it takes a concerted effort to actually put down woo. While they have no standards of evidence, and pretty much just make stuff up on the fly, we are bound by science and our conscience to present information that we can actually back up.

Well, antiscience is taking major body blows the past week or so, and it’s a wonderful, wonderful thing to see. It started with Newsweek taking down the quackery promoted by Oprah Winfrey, and has taken off from there:

1) Reader’s Digest jumped on the anti-Oprah ride… and when the milquetoast middle-of-the-road offend no one RD takes you on, it’s time to rethink your very existence.

2) Deepak Chopra — who couldn’t find reality with both hands, a compass and, evidently, the aid of centuries of scientific advancement — ran to Oprah’s defense, and, as usual, mangled more logic in one essay than can be humanly possible without the aid of quantum healing. Massimo Pigliucci magnificently takes him down, as did JREF’s Jeff Wagg at the Swift blog.

3) The Australian government has ruled that Arnica Montana, a homeopathy company, falsely advertised the efficacy of its product — which, in the case of homeopathy is everything they advertise — and they had to post a humiliating retraction. I weep non-diluted tears for them. Dr. Rachie has more info. Also, Steve Novella has written a lengthy and complete destruction of homeopathy on his NeuroLogica blog. If you are a homeopathic believer and feel you must spout your undiluted nonsense in the comments below, read his essay first, because if you make any of the claims he debunks I will allow everyone free reign to mock you. Because that’s better than allowing babies to die due to homeopathy.

4) Simon Singh is being sued by the British Chiropractic Association because he wrote about their "bogus" claims. BCA vice-president Richard Brown then posted a flailing essay titled In Defence of Chiropractic in New Scientist magazine, a piece laden to the hilt with astonishingly poorly thought-out logic. Apgaylard thoroughy dismantles the claims from Brown, leaving the emperor looking a little naked out there.

This kind of antiscience antireality antihealth garbage will always be with us, but I can hope to help amplify the chorus of voices being raised against them. It’s important, as I have been hammering home for months. They will never rest as long as people credulously accept their claims, so we need to make sure as many people as possible examine their claims as critically as possible.

Today in the News (15 Jun 09), Part 2

Since IVAN3MAN took care of evolution news today, I'll just post a couple quick other stories. I also wanted to let you all know that I had a successful interview with the UBC Freethinkers. The podcast will be broadcast in about three weeks, and I'll be sure to let you all know.

So in general news (on vaccines and autism):
A mother vaccinates one son, and doesn't vaccinate the other, yet they both turn out to have autism (Sorry, the original story disappeared after I posted it, so we have this version instead, the gist is the same). HOW CAN THAT BE!? Perhaps vaccines have nothing to do with it, and there are other factors at work? Just because someone has taken the whole idea of a cause for autism hostage doesn't make them any more correct. If anything, the anti-vax pro-disease crowd has set back reliable and fruitful research by insisting that their anecdotes have some validity. The research community ends up fending off these red herrings instead of going after fruitful research. So not only are they a public health hazard, but they are inhibiting research on the very thing they are the most upset about. Is your irony meter pegged?

An interesting blog post from an MD asking the "fake autism experts to put up, or shut up". Imagine that, the anti-vax pro-disease movement is just making things up on the fly, and out and out lying. Nice "Spinal Tap" reference in the article too. ;)

I also enjoyed this article about the vast differences in the ways that the human brain processes information. It gives insight into some more relaible ways to communicate and socialize people with autism spectrum disorders. Item #6 is the one specific to autism, but I wonder how many of these other insights may help?

This article discusses some miRNA therapies that can help with cancer, schitzophrenia, autism, and perhaps other disorders. The key takeaway here is that again this is pointing to a genetic link.

Oh, I just saw this short bit. Look at exactly what the last line says. Rather telling I think if you compare it to actions of others capitalising on this fake controversey.

Today in the News (15 June, 2009)

Evolution

Latest report from Science Daily (June 15, 2009):

Gene Evolution Process Discovered

One of the mechanisms governing how our physical features and behavioural traits have evolved over centuries has been discovered by researchers at the University of Leeds.

Darwin proposed that such traits are passed from a parent to their offspring, with natural selection favouring those that give the greatest advantage for survival, but did not have a scientific explanation for this process.

In new research the Leeds team reports that a protein known as REST plays a central role in switching specific genes on and off, thereby determining how specific traits develop in offspring.

The study shows that REST controls the process by which proteins are made, following the instructions encoded in genes. It also reveals that while REST regulates a core set of genes in all vertebrates, it has also evolved to work with a greater number of genes specific to mammals, in particular in the brain – potentially playing a leading role in the evolution of our intelligence.

Says lead researcher Dr Ian Wood of the University's Faculty of Biological Sciences: "This is the first study of the human genome to look at REST in such detail and compare the specific genes it regulates in different species. We've found that it works by binding to specific genetic sequences and repressing or enhancing the expression of genes associated with these sequences. [...]

Click on the above link to continue.

Weekend News (13-14 June, 2009)

Evolution

Here is an interesting news article from Science Daily (June 12, 2009) on how life could have arisen on Earth:

Simple Chemical System Created That Mimics DNA

A team of Scripps Research scientists has created a new analog to DNA that assembles and disassembles itself without the need for enzymes. Because the new system comprises components that might reasonably be expected in a primordial world, the new chemical system could answer questions about how life could emerge.

The work, reported in the journal Science, might also be a starting point on the way to exotic new materials that repair themselves or transform in response to their environment.

Scientists are both bemused and fascinated by the question of how life could have arisen on Earth. One of the most prominent theories is that, before the emergence of DNA, the earliest forms of life used RNA to transmit their genetic codes. The late Leslie Orgel, a co-author of the new paper, first suggested this idea, known as the "RNA World."

One of the theory's challenges is that RNA is still so complex that many researchers [hypothesize] something still simpler must have preceded it. "I have been working for years to learn what replicators and genetic systems might have come before the advent of the RNA World," says team leader of the new research Professor Reza Ghadiri, a Scripps Research chemist.

One key focus for Ghadiri's team has been amino acids' potential primordial role. In 1996, the group showed for the first time that amino acid strands, or peptides, can self-replicate under enzyme-free conditions. In the current work, the Ghadiri lab extends this focus by creating another type of information system that might be capable of something akin to Darwinian evolution. "This work is a beginning step toward that goal," says Ghadiri. [...]

Click on the above link to continue.

Today in the News (12 Jun 09)

Vaccines:
Another "I told you so!" in the local news, whooping cough is on the rise in my neck of the woods. No deaths (yet), but this is disturbing.

And Bill and Melinda Gates get it. They want to help get vaccines to the poor. Just read the linked story, and look at the number of people who die worldwide from these diseases.

Autism:
Not much news here. The US Government is still moving forward with a promise to fund autism research to the tune of nearly $200 million a year. While this is encouraging, I must wonder why autism is the ONLY disorder singled out for this funding, while diseases such as heart disease, diabetes, and such which cost the US billions more than autism. Don't get me wrong, it is a great boon to autism research, but is it done for a popularist and pandering reason as opposed to reality and data?

Since autism is often labeled as an epidemic, I found this review of some of the psychology behind "fear epidemics" rather informative. Like Kay said in Men in Black, "A person is smart. People are dumb, panicky dangerous animals and you know it. Fifteen hundred years ago everybody knew the Earth was the center of the universe. Five hundred years ago, everybody knew the Earth was flat, and fifteen minutes ago, you knew that humans were alone on this planet. Imagine what you'll know tomorrow." I just love that quote, and it's so true!

Evolution:
I am linking to this article mainly because of a descriptive sentence, "This is significant because it is an example of how existing components can be used in evolution to make something completely new." How cool is that?!

While in general boring, this news about the different types of mussels that are found in the US great lakes does speak to evolutionary pressures. Since these are invasive species, understanding them more should help us deal with them better.