S. aureus found in meat and poultry

Posted on April 28, 2011 by Michael

Staphylococcus aureus has been found in U.S. meat and poultry at alarming rates:

Nearly half of the meat and poultry samples — 47 percent — were contaminated with S. aureus, and more than half of those bacteria — 52 percent — were resistant to at least three classes of antibiotics, according to the study published today in the journal Clinical Infectious Diseases.

This is the first national assessment of antibiotic resistant S. aureus in the U.S. food supply. And, DNA testing suggests that the food animals themselves were the major source of contamination.

I’m mostly posting this because I’ve recently been working with various bacteria, including S. aureus. One of the biggest problems with them – indeed, with any major and most minor bacteria species – is that they evolve quickly in response to the antibiotics we use against them. This research specifically looked at resistance, and the numbers are surprising. Compounding the issue, there are really only six or so major companies that work to develop antibiotics in the U.S. today. Though our government is a big corporate welfare bitch, our direct government investment in this sort of research is non-existent. That really makes no sense. It is government funding that has long been a huge driving force behind the science of the 20th century, and this is especially true where both lives and profits are at risk – private businesses will always opt to risk the former, not the latter. Given how quickly bacteria evolve to get around antibiotics – resistance has been detected in the very same year the antibiotics have been developed in some cases – it would be good science and our health if we started investing more. A lot more.

That said, there are preventative measures that need to be addressed. First – and we need government again – limit what farmers can give livestock. Of course resistance will evolve if we keep giving cows and chickens antibiotics at such high rate. Second – yep, government again – tighten food-handling protocols in meat markets, including supermarkets. Given the $8 an hour supermarkets pay their employees, I doubt people in that field will give two shits, but every little bit helps (especially before the food gets to that point). And finally – we might not need government to do all of this one – educate the general public, i.e., cook your food at recommended temperatures, wipe down counters, and other basic things civilized people ought to be doing without being told.

Filed under: Evolution, News | Tagged: , , , | 16 Comments »

S. aureus found in meat and poultry

Posted on April 28, 2011 by Michael

Staphylococcus aureus has been found in U.S. meat and poultry at alarming rates:

Nearly half of the meat and poultry samples — 47 percent — were contaminated with S. aureus, and more than half of those bacteria — 52 percent — were resistant to at least three classes of antibiotics, according to the study published today in the journal Clinical Infectious Diseases.

This is the first national assessment of antibiotic resistant S. aureus in the U.S. food supply. And, DNA testing suggests that the food animals themselves were the major source of contamination.

I’m mostly posting this because I’ve recently been working with various bacteria, including S. aureus. One of the biggest problems with them – indeed, with any major and most minor bacteria species – is that they evolve quickly in response to the antibiotics we use against them. This research specifically looked at resistance, and the numbers are surprising. Compounding the issue, there are really only six or so major companies that work to develop antibiotics in the U.S. today. Though our government is a big corporate welfare bitch, our direct government investment in this sort of research is non-existent. That really makes no sense. It is government funding that has long been a huge driving force behind the science of the 20th century, and this is especially true where both lives and profits are at risk – private businesses will always opt to risk the former, not the latter. Given how quickly bacteria evolve to get around antibiotics – resistance has been detected in the very same year the antibiotics have been developed in some cases – it would be good science and our health if we started investing more. A lot more.

That said, there are preventative measures that need to be addressed. First – and we need government again – limit what farmers can give livestock. Of course resistance will evolve if we keep giving cows and chickens antibiotics at such high rate. Second – yep, government again – tighten food-handling protocols in meat markets, including supermarkets. Given the $8 an hour supermarkets pay their employees, I doubt people in that field will give two shits, but every little bit helps (especially before the food gets to that point). And finally – we might not need government to do all of this one – educate the general public, i.e., cook your food at recommended temperatures, wipe down counters, and other basic things civilized people ought to be doing without being told.

Filed under: Evolution, News | Tagged: , , , | 16 Comments »

To kill a mocking…bat

Posted on April 21, 2011 by Michael

I would say I have at least a cursory interest in every animal I’ve ever read about or seen in a documentary. Life is life. It’s all interesting. (Read Richard Dawkins’ The Ancestor Tale.) But for the past 3 years (as of this July), I’ve had a special interest in bats. You see, I deal with an invasion in my ceiling of the little things every summer. I’m not sure if it’s really beautiful or just creepy hearing them scamper about, but I do enjoy laying awake listening to them. At least, I enjoy them until they manage to get inside. At that point it’s a matter of catching them with a blanket before the cats catch them with a set of claws and teeth. It wouldn’t be so bad if 1) I didn’t have to get my indoor cats preventative shots I otherwise wouldn’t have bought and 2) there wasn’t the ongoing white nose syndrome epidemic going on with bats. The disease so far appears to be limited to bats – decimating huge colonies – but since it isn’t very well understood at all yet, I don’t like the idea of exposing my animals to it (or myself).

But even with limited understanding, an interesting question is raised. Can we help to prevent its spread? One line of thinking says we can by destroying infected bats. But others are calling on the power of evolution:

Kentucky wildlife officials acted quickly when a confirmed case of the disease was found in a bat in Trigg County recently. They euthanized 60 “highly suspect” bats that were “not expected to survive,” they said Wednesday…

Local and national experts, however, believe euthanizing infected bats may not prevent the spread of the disease and could be “counterproductive” to the effort.

Dr. Merlin Tuttle, founder of Bat Conservation International, said white nose syndrome has reached epidemic levels, killing more than 1 million bats since 2006. He said in cases, like this one, where a disease has a very high mortality rate, it is important to see if some infected bats are able to fight off the disease. That way, those with immunities to a disease are able to pass on that ability to their offspring, eventually re-populating the species with bats that can withstand the disease.

“If you kill every bat that gets (the disease), it’s pretty hard to see who survives,” said Tuttle, who has studied bats for more than 50 years. “Just because you get sick, it doesn’t mean you die.”

It isn’t an easy call. Bats are dying in record numbers. Something clearly must be done. Evolution may provide the doing – after all, bats have been around for 50-55 million years – but if humans can successfully intervene, then we should. The problem is that we just don’t really know how to go about it.

Filed under: Evolution, News | Tagged: , , , , , | 2 Comments »

Revelation TV interview of Richard Dawkins

Posted on March 20, 2011 by Michael

My two favorite parts happen between 36 and 40 minutes. First,

Conder: Am I just deluded?

Dawkins: Probably, yes.

Second, shortly thereafter Conder cites the fulfillment of prophecies, especially those that come from Micah, as one of his big reasons for initially being attracted to the Bible. It’s hilarious. As I’m sure all good Christians know, the gospels were often poor attempts to fulfill those prophecies. That’s the case with the birth of Jesus.

Anyway. The interviewer is pretty awful, but Dawkins’ parts are good.

Filed under: Atheism/Humanism, Evolution | Tagged: , , | Leave a comment »

What is ‘junk DNA’?

Posted on March 5, 2011 by Michael

I’m always hearing people bring up the modern understanding of ‘junk DNA’ as if it somehow lends evidence to the existence of God. It’s not an argument I really get. Whether most of an organism’s DNA is needed or not doesn’t magically disprove evolution. Maybe people just don’t get the concept, I don’t know. I’ll try and give a brief explanation.

About 30 or 40 years ago it was understood that most of the human genome was composed of DNA that served no discernible purpose. That understanding changed with time, morphing from a position of no purpose to one where most DNA was noncoding. This was partially a technical change. Most DNA is noncoding; it doesn’t produce proteins. “Junk” is a misnomer in this context. But we’re discovering more and more that previously deemed purposeless DNA actually does have a function. Often enough it is important in regulation. But still, some 95% of our DNA has no function at all. We may be finding that more of it serves some purpose than we previously thought, but the fact that most of it is useless remains.

I bring this up because of a recent post I saw on an anti-science website (better known as the inspiration for my still-new Punching Bags series – I use it as a hunting ground now). What I find so entertaining about these creationists and their infatuation with junk DNA is that one of the reasons biologists (not creationists, of course) are able to determine that DNA has a function is because of evolution. Sometimes we can directly determine a function through experiment and observation, but much of the time we rely upon inference. DNA which is noncoding yet none-the-less conserved is said to have some sort of function. It must. It makes no sense for a given sequence to exist over millions of years and across distant lineages if it doesn’t serve some function. Of course, this is no problem for those of us on the side of science. Everything really does make sense in the light of evolution. (And you thought that saying was just rhetoric.) But this does pose a problem for creationists. While they’re trying to inanely deny that most of our DNA is not usefully transcribed, they are necessarily relying upon the fact of evolution – the very thing they want to deny.

If it wasn’t for the harm to all of science they cause, I would more easily delight in pointing out how ill-considered creationist ideas really are.

Filed under: Evolution | Tagged: , | 10 Comments »

“Is natural selection random?”

Posted on February 20, 2011 by Michael

One of the most common series of search terms that gets people to FTSOS is the title of this post. Most people end up clicking my article on why natural selection is not random; I’m not a huge fan of that piece. It was originally written for a local weekly paper (which changed ownership as I finished), not a blog. What’s more, it is very far from being succinct. I want to rectify that issue in this post.

So is natural selection random? No. Why not? The answer is simple: Natural selection is the pressure placed on a population and the change that happens in response to that pressure. Whereas the exact pressure is in part random in regards to any given population, exactly how a population responds follows some basic rules. Now, the reason I say the pressure is only random “in part” is because first and foremost I’m referring to changes in the environment that happen without regard to life. The rising of a mountain range is one example. But at the same time, other changes that might occur are in response to the direction of a population. For instance, it often pays to be the biggest and baddest member of a species for males, but instead of responding by becoming all the bigger and badder, some members might just become tricky. Some octopi, for example, will trick guardian males into believing they are just another female, gaining them access to the real female. This pressure isn’t entirely random since it is a response to the evolutionary state of a population. That is, becoming tricky is a response to being big and bad, and becoming big and bad was not itself random. But why? Well, I’m glad you asked:

Selection is a biased reaction to a given environment. This is specifically with regard to life: those that are able to exploit their environment best (and I really just mean ‘well enough’) are the ones that are going to survive. If it was all just random, then we would see no bias: We wouldn’t see a species trend in one way or another, beneficial genes would hardly ever become common, and we would never be able to make predictions. But what we see are trends and an increase in beneficial genes (and the elimination of deleterious genes) and we make predictions all the time. It is because of biased genetic reactions in populations that we call natural selection non-random.

I wouldn’t mind going on and on, but I said I want to make this succinct, so I will end with just one final but important point: The non-biased genetic reactions that happen because of natural selection must be measured across a population and through generations. If a creationist someone starts talking about natural selection being random and pointing out individual responses to the environment, then we might not be talking about the same evolutionary mechanism anymore. Everything that happens within evolution is happening to populations. Individuals do not evolve. So natural selection is the differential survival of individuals (or genes, depending on your perspective), but it is measured through time and within the context of a population.

Filed under: Evolution | Tagged: , , , | 1 Comment »

A basic point about evolution

Posted on February 7, 2011 by Michael

Evolution is an entirely natural process. It occurs through well understood mechanisms for which we are gaining ever improving detail. The belief in theistic evolution runs counter to all this; it is not compatible with the theory. Yes, yes, there are people who say they accept both their interventionist god and evolution and therefore their views are not contradictory, but that holds no relevance here. Things don’t become compatible simply because a lot of people believe them simultaneously.

In order for one’s views to be consistent with evolution, one can only hold two positions: atheism or a sort of deism. By “a sort of deism” I mean either exactly deism or something where, okay, there is a god who intervenes in human affairs, dictates our morality, and does all that other magic bigoted thought-crime sort of thing, but this god does so incidentally. That is, since no particular form of life, much less characteristic, much less species, was ever destined to exist by any law of biology, a god which it is believed made humans (or intelligent life, a la Miller) inevitable is necessarily false. Only a god which had no part in evolution is tenable; evolution is a miracle free process.

So let’s break it down:

Atheism: Entirely compatible with the theory of evolution. The process of natural selection is miracle free and excludes all directed intervention.

Traditional Deism: Compatible, but likely unsatisfying. By “traditional” I mean the deism which says there was a creator with intention that began the Universe, but that creator’s interest ended there.

Other Deism: Compatible, but still unsatisfying. I use “other” because there is no particular name for this sort of deism as far as I am aware. This is the deism which says we have a moral lawgiver and all that swell BS, but it can only be incidental. The theory of evolution tells us that humans were not destined to exist, therefore we cannot say that this interventionist god planned on us, as if we’re somehow special.

Theistic evolution: Not compatible. No species are destined to exist. That includes humans.

Creationism: Moronic anti-science nonsense. It isn’t compatible with any major branch of science.

I have excluded agnosticism because it doesn’t mean much to say that this or that is or is not compatible with “idunno”.

Filed under: Evolution | Tagged: , , , , | 33 Comments »

Humans may have left Africa sooner than once thought

Posted on January 28, 2011 by Michael

I said my views on evolution are always evolving. This is a good example of that.

Modern humans may have left Africa thousands of years earlier than previously thought, turning right and heading across the Red Sea into Arabia rather than following the Nile to a northern exit, an international team of researchers says.

Stone tools discovered in the United Arab Emirates indicate the presence of modern humans between 100,000 and 125,000 years ago, the researchers report in Friday’s edition of the journal Science.

While science has generally accepted an African origin for humans, anthropologists have long sought to understand the route taken as these populations spread into Asia, the Far East and Europe. Previously, most evidence has suggested humans spread along the Nile River valley and into the Middle East about 60,000 years ago.

“There are not many exits from Africa. You can either exit” through Sinai north of the Red Sea or across the straits at the south end of the Red Sea, explained Hans-Peter Uerpmann of the Center for Scientific Archaeology of Eberhard-Karls University in Tuebingen, Germany.

“Our findings open a second way which, in my opinion, is more plausible for a massive movement than the northern route,” he said in a telephone briefing.

These findings are always interesting, but it takes so much evidence to come to any sort of conclusion that the theories put forth are always so tentative. We can say humans probably left Africa earlier than previously thought, but speculation on a new route is less solid.

One recent theory I recall hearing is that humans and Neanderthals once interbred. There is some evidence for it, and just last year some good DNA evidence was uncovered showing as much. In fact, I would go so far as to confidently proclaim that the evidence solidly shows humans interbred with Neanderthals very early in the human exit from Africa. Beyond that, I very much doubt there was interbreeding; the Neanderthals in all probability died out as a unique species, unable to breed with H. sapiens.

I mention this theory because the first thing that popped into my mind upon reading the first few paragraphs of the article was how long it would take until someone suggested Neanderthals may have been responsible for the toolmaking.

The techniques used to make the hand axes, scrapers and other tools found at Jebel Faya in Sharjah Emirate suggest they were produced by people coming from somewhere else, said Anthony E. Marks of Southern Methodist University in Dallas, adding that there are similar tools made about that time in East Africa.

“If these tools were not made by modern man, who might have made them?,” Marks asked. “Could Neanderthals have made them?”

Neanderthals were mainly in Europe and migrated into Russia but “there is no evidence for any Neanderthals south of that” zone at that time, he said. “To suggest one group of Neanderthals took a turn south and went several thousand kilometers … seems to me a very difficult explanation and one that doesn’t follow any reasonable logic.”

I have to agree with that assessment of the data. Humans moved towards Neanderthals, plausibly going through the areas of this recent discovery, not the other way around. Now that we have evidence left by our ancestors, this adds a new route humans took when leaving Africa. I find the scenario plausible, even likely. It still isn’t certain, but there is now some good evidence for it.

Filed under: Evolution | Tagged: , , , | 5 Comments »

‘What would change your view on evolution?’

Posted on January 27, 2011 by Michael

I hear that question posed from time to time. Sometimes it is directed at me, but more often I hear it directed towards established (and often famous) scientists. It’s usually a product of creationist rhetoric where the answer doesn’t really matter. Regardless, it is an interesting question.

What would change my view on evolution?

It depends what is meant by “change”. My view on evolution changes quite frequently, actually. Sometimes it’s a qualitative change: the relationships between our known ancestral cousins are always shifting ever so slightly. Often, there is little consensus about where to place certain members of the genus Homo on the evolutionary tree. As new evidence is found, as more research is done, as further facts come to light, my views are always changing on that aspect of evolution.

And then there are quantitative changes. One excellent example comes from the discovery of tetrapod footprints. That discovery pushed the evolution of tetrapods back about 18 million years. All the relationships between species of that general time period stayed the same, but our view of when tetrapods began to populate the land changed.

And then there are all sorts of other changes, like recently when it was shown that natural selection works differently on allele fixation in sexually reproducing populations versus more simple asexual populations. (That was also a qualitative change, but on the genetic, not taxonomic, level.)

So if that is what is meant by “change”, then there are all sorts of examples that show how my views on evolution are, well, evolving. The same can be said of biologists around the world. But what if by “change”, the real question being asked is, What would make me dismiss evolution? Then the answer is very different.

As I recently explained, a basic fact of science is that it does not tend to operate on individual studies. It requires a body of evidence to change views. For example, I reject a connection between cell phone use and cancer. Studies have shown possible links, but they have been far from conclusive, weak even. And more importantly, there is a body of evidence showing no significant link. I’m going with the evidence in bulk, not the individual packaging. This relates directly to the question of what it would take to get me to dismiss evolution because there is a famous quote by J.B.S. Haldane I had in mind when starting this post. When asked what it would take to change his mind, he retorted,

Fossil rabbits in the Precambrian.

But that wouldn’t change my mind. My very first suspicion would be fraud; I suspect little more from creationists (and we know how much they would be promoting such a discovery). But let’s say it came from a reputable research team, then what? I would admittedly be perplexed. There is no reason a fossil rabbit ought to be found in that era, but that doesn’t mean we get to throw out such a well established theory as evolution. We know evolution is true insomuch as we know gravity is true. It would necessarily take more than a few rabbit fossils to alter the unifying theory of biology, just as it would take more than an apple falling up for us to alter the theory of gravity. Even if we could never explain the fossils satisfactorily, I would have no doubts that evolution still formed the basis of my field of choice.

What would change my view would be the discovery of a number of fossils in all the wrong places. We would need to start finding mammals and birds dating back 800 million years; we would need to see dinosaur fossils embedded in the rocks of 20 million years ago; we would, yes, need to see rabbit fossils in the Precambrian. No, I don’t need these specific examples, but I do need these sort of examples. I don’t want just individual anomalies that fly in the face of modern theories. I need more than that: it takes a body of evidence to start changing my view. Because that’s how science works.

Filed under: Evolution | Tagged: , , , , , | 13 Comments »

Tasmanian devils may go extinct

Posted on January 22, 2011 by Michael

Just over a year ago I wrote about the facial cancer that has been so deeply afflicting the Tasmanian devil population. Things have only become worse.

Tasmanian devil cancer is threatening to wipe out the entire species, and researchers say there are only around 2,000 left in the wild, according to Scientific American.

An infectious type of cancer called devil facial tumor disease first appeared in 1996 and has killed off 90 percent of the population of the famed carnivorous marsupial.

Scientific American notes that in the last nine months, the cancer die-offs have increased from 70 to 90 percent of the population, leaving researchers with no other choice than to fear the worst.

As I wrote last year (in this post), the disease ought to be considered a separate organism, free to undergo its own evolution. That’s exactly what has happened.

And to make matters worse, the cancer has turned into 13 different strains since it was first spotted, Sky News reports.

“The disease itself is a living organism and it wants to stay alive and it fights to stay alive,” David Schapp, a breeder at a Tasmanian devil facility, told Sky. “So when it meets devils that show some form of resistance to it, the disease evolves and changes so it gets to live and continue.”

This certainly is not the first time cancer has acted this way, but that doesn’t mean this is any less horrific. The most likely way the Tasmanian devil is going to be saved will be through human intervention. Fortunately, that is exactly what is in the works with the creation of temporary habitats. It isn’t the most ideal situation, but it is the best solution.

Filed under: Evolution, News | Tagged: , , , , , | 2 Comments »

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