Pope adds a lot more people on the way to hell

I heard this on the morning news and thought I just had to bring it up here as the Pope has added a whole bunch of new sins that will send you to hell. Some of these I can somewhat understand, but a couple are just a little narrow-sighted in their intention:

“You offend God not only by stealing, blaspheming or coveting your neighbour’s wife, but also by ruining the environment, carrying out morally debatable scientific experiments, or allowing genetic manipulations which alter DNA or compromise embryos,” he said.

Morally debatable experiments? Does that mean anything you disagree with? The part about genetic manipulations of embryos could be understood from the point of view of making humanity into some sort of “perfect” vision of some deranged group or individual, but there are many valid reasons to manipulate the genome of an embryo such as in the case of hereditary genetic diseases. These sorts of blanket rulings are not going to be conductive to bringing people back to the Catholic church or convincing anyone that the church isn’t still sticking itself firmly in the dark ages.

Edit: Dr. Myers has some more commentary here.

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One step forwards and two steps back

So it seems that Bush and company have decided that they are no longer forcing much of their AIDs money to go into abstinence only campaigns. Instead they now require ‘justification’ if less than 50% of money doesn’t go into abstinence or faithfulness campaigns, which may sound reasonable but it will depend in my view on how stringent they are (and what conditions they stick on that). The ABC (Abstinence, Be faithful and use Condoms) campaign in Nigeria showed this can be a very effective approach, but preaching abstinence and faithfulness alone is utterly worthless for doing much of anything. If this is just another way of enforcing more money into going into campaigns that clearly don’t work well rather than sensible sexual education and prevention campaign (and that means encouraging things like condom use) then it’s just going to make things worse.

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Turtles all the way down for Florida

With Florida deciding if they should adopt good science standards or insert nonsense from the usual suspects, I think a quick reminder of my previous “turtles all the way down” essay is in order. Despite the age of this and that it’s a fairly common anti-ID argument, I’ve never really seen it adequately refuted. One particular argument (well cop-out really) is that aliens that could design us don’t need to be complicated themselves and could have evolved elsewhere. Of course, when asked what these aliens could look like, what ID predicts the environment they evolved in should be and what methods they could have used (being ‘simpler’ than us, who must have been designed you see) usually results in the crickets chirping. I still stand by that ID is nothing more than creationism redressed to make it more palatable to being inserted into American classrooms after creationisms heavy defeats in key court cases in the early and late 1980s. Ultimately, any ID proponent that wants to argue space aliens has to somewhere demonstrate where these space aliens may have come from and why they were able to evolve by natural means, but life on earth could not (again, another question that is merely greeted with the sound of crickets). In any event, this repost is for you Florida ❤

Turtles all the way down.

Around the net I’ve seen this expression come up called ‘turtles all the way down’, usually referenced to intelligent design. The term comes from a story, of unknown source as it seems to come up often from different people, where essentially a famous lecturer was giving a talk on astronomy. After he was finished a little old lady came down and told him he had it all wrong.

“The world is really on the back of a giant tortoise” the woman said to which the scientist asked, in an attempt to stump her most likely, “Well then, what is the tortoise standing on?” To this the lady triumphantly replied “You’re very clever young man, but it’s of no use – it’s turtles all the way down”.

In many respects this is the problem that intelligent design faces when it proposes a ‘designer’ is natural. For example, when we take Dembski mathematics, fancy as they are and apply it to the designer we find, unsurprisingly, that the designer must himself be designed. If we do the same thing again, we find that each designer in turn requires another designer. Eventually, we have an infinite regress of designers, each one designing the previous one; turtles all the way down in other words.

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Nature and HIV pessimism

This news article in Nature, entitled, HIV can ‘never be cured’ caught my interest pretty much immediately as it describes some interesting new research on the HIV virus and for its unusually pessimistic title. For one thing, it’s true that HIV is a very tricky virus to get rid of because it attacks the immune system that a vaccine and the host needs to actually destroy the virus to begin with. Additionally, as if things weren’t bad enough, HIV is pretty crafty and likes to hide in a wide variety of places such as inside T-cells (the generals of the immune system for a rough comparison), follicular dendritic cells (which store antigens for restimulating memory T-cells) and apparently even the gut (1). Being able to infect the gut causes a few problems, one of which is that the current top of the line anti-retroviral drugs don’t seem to be able to destroy this gut reservoir of HIV. This leads to a continual re-infection of the rest of the body from the HIV population in the guts lymphoid (immune) tissue.

While a serious problem, I don’t view this as making HIV ‘incurable’ by any stretch, just it makes things considerably more complicated. It should mean rather than being a result that makes us more pessimistic, instead it should be taken as a result that bolsters our understanding of how HIV causes an infection and better design a vaccine/new drug regimen. For example, armed with this knowledge a potential vaccine may have aspects that help target mucosal immunity and could [theoretically] inspire the gastrointestinal part of the immune system to help destroy the virus: or even prevent the early reservoir from being able to form abrogating an infection. Likewise, current anti-retroviral treatments could have new drugs or altered existing drugs that can target the virus in the gut lymphoid tissue, helping to further prevent reinfection with the virus.

It should be conceded that HIV being able to form a relatively protected reservoir in the gut does make life a whole lot more difficult, I don’t think it’s a result that warrants undue pessimism by any stretch. Knowing something you didn’t know before and couldn’t account for, doesn’t make HIV any more ‘incurable’ than it was before, instead it should be taken as a new way of thinking and attacking the problem at hand. Statements like declaring it ‘incurable’ are not going to help anyone anytime soon.

1) Chun, T.-W. et al. J. Infect. Dis. doi:10.1086/527324 (2007).

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Darwin day

Happy Darwin day to everyone and have a good time reflecting upon the role of this great mans theory in enhancing our understanding of biology today! Scientificblogging and the Pandas thumb will both be collecting some interesting posts on Darwin over the day or so. One I’ve found that I particularly liked, was by Josh Rosenau describing Abraham Lincoln and how Darwin viewed the Norths movement to abolish slavery in the United States. Although not on the scientific achievements of Darwin, it’s an interesting piece of history that I didn’t actually know myself before now.

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Farm animal cannibalism (Repost)

[This is a repost from my previous blog that’s semi-relevant to another topic I’m going to bring up in the near future on this blog. It’s also a cheap way of getting postcount++ while I don’t have the time to make a totally new post. Enjoy!]

Cannibalism is one of those practices that, at least as far as humans go isn’t very high on the list of things that are socially acceptable. One of the numerous problems with cannibalistic practices is the transmission of diseases, after all what infects dinner is just as easily going to infect the cannibal. It should be reasonable common sense as a result not to feed a farmed animal the remains of their fellow animals. This would greatly aid the spread of an infectious microorganism through a herd and possibly even rapidly increase virulence (which is often directly correlated to the ease of transmission).

The case example of why this practice shouldn’t be performed, with any animal, is the dramatic outbreak of bovine spongiform encephalopathy (BSE) in Britain. BSE was found to be spread by an infectious protein called a prion, which is predominantly found in the brain and spinal matter of the remains of cattle. Worse, these parts were frequently fed back to other cattle as a supplement to their feed, providing an easy method of transmission for the infectious prions. The worst part of the entire discovery was not just that other cattle could be infected in this manner, but the potential spread of the disease between beef from infected cattle and humans. This led to the culling and suffering of a large number of animals and an overall ban on British beef that lasted a considerable time.

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Dr. Simmons has lost his grip on reality.

Dr. Simmons, who is the man best known for his hideously terrible arguments he put forward against PZ Myers in their recent debate, is apparently doing a Black Knight. He accuses PZ Myers of a variety of things, such as not paying attention to the points he raised, bearing in mind that Dr. Simmons never raised any points that were actually valid or not easily contradicted. Simmons opined:

Before the recent KKMS (MN radio) debate, Dr. P.Z. Myers blogged on Pharyngula that he would decimate me. Within minutes of the shows conclusion, he blogged that he accomplished his goal, never conceding a single point from an hour long show. It is worth ones while to read his blogs and those that follow as they readily speak to the character of these folks, much moreso than I could ever do. Richard Dawkins was also quick to compliment the professor and add to the feeding frenzy. Again, no concessions. They had their hearing aids turned off before the show even started.

Of course, we should point out at this point that even diehard ID supporters believed that Dr. Simmons came off looking completely clueless and indeed got ‘decimated’ by Dr. Myers. When even your own side believes you performed horribly and not just those opposed to your viewpoint, that probably means you did a terrible job: not that your opponent didn’t listen. Dr. Simmons goes through with another howler about the current state of understanding about whale evolution:

Could it be the five or so fossil pieces from dog-size animals that represent intermediate species between land animals and the quadrillion-cell whale with unexplained tons of blubber, communication skills that span thousands of miles, a windpipe separate from the esophagus (unheard of in land animals), segmental decompression, a heart the size of a Volkswagon, ability to dive thousands of meters deep or eat a krill diet?

Starting off with a factual inaccuracy is not a good way of making a point, clearly demonstrating that Dr. Simmons has never actually bothered to look into whale fossils at all or he would be familiar with many larger transitionals like Basilosaurus, which is around 15 meters in length. If he was trying to demonstrate he learned absolutely nothing from his debate with PZ Myers, he has certainly gone out of his way to prove that. He then adds the standard creationist fallacy of an argument from improbability/argument from incredularity, which is basically him stating that “I cannot see how this evolved, therefore God/Design/whatever”. This isn’t even an argument really and he continues it onto his developmental argument, which again boils down into “I can’t see how you developed, therefore God!!! I R IRREFUTABLE!!” etc. I’m sorry, but that’s not even an argument at all.

I think that the criticism Dr. Simmons suffered from his own side, the hammering he got on air from an opponent that actually knew what they were talking about and the subsequent bizarre post have caused him to lose some of his grip on reality.

Edit: It’s worth noting that Dr. Simmons in his whale rant never actually finishes whatever he was trying to say. He never refutes that there are actually early transitionals in the whale fossil line, he just brings up the point and then goes into a rant about how complex modern whales are (while simultaneously forgetting to address the original mentioning of transitional fossils, fossils he claims don’t exist at all).

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Native New Zealand freshwater crayfish

A couple of weeks ago I got the opportunity to go and have a wander around a stream near a friends house. After poking at various insects and other creepy crawlies, it occurred to me to have a look in the water and see if I could find anything a bit different than the usual insects I find. It just so happens that I found this fellow (click images for full sized picture..theoretically anyway):

This fellow is a freshwater crayfish, one of two species in New Zealand Paranephrops zealandicus, or more commonly known as the Southern Koura. The other species, rather boringly enough, is simply called the Northern Koura (Paranephrops planifrons) and is rather similar to the Southern Koura, but is often of a smaller size. Moving some rocks around revealed something moving about in the water and closer inspection revealed several Koura wandering about. Catching them was a little tricky, as they are extremely fast and stirring up sediments makes life much harder, but in the end I succeeded (for SCIENCE!). Once ready for his photoshoot this guy* was rather happy for the most part to sit up for the camera and have his photograph taken, but there was one rather dramatc incident towards the late afternoon.

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Update on the research blogging controversy

There is a further update on the discussion the other day about Casey Luskin using the research blogging icon inappropriately on the official research blogging news site here.

I talked privately with science ethicist Janet Stemwedel, and she agrees that the blurring of the distinction between what’s supported by the article itself and what constitutes the blogger’s personal opinion is problematic. In this case, when Luskin refers to “the evidence,” what evidence could he be referring to, if not the evidence supposedly offered in Orgel’s article? Yet Orgel does not present any evidence that “the complexity of life requires an intelligent cause.” The blog post itself should make it clear that this final assertion is Casey’s alone, not Orgel’s. We shouldn’t have to wait for Luskin’s assertion that this was only his personal opinion, especially when he still hasn’t modified his original post to make that clear.

Which is pretty much what I think as well.

 

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Animalcules: A history lesson

Although some visitors may wonder if the blogs title “Animalcules” is spelt incorrectly, as it certainly is a funny way of spelling “animals”, it’s actually a homage to one of the most significant early microbiologists, Antoni van Leeuwenhoek. Van Leeuwenhoek was a remarkable man, as he observed many previously unknown microorganisms, most importantly bacteria, without having had any formal scientific training and in fact was a professional draper (fabric merchant). Born in Delft, Holland on October 24, 1632, he eventually came to own his own drapery and around 1668 had began to produce his own simple microscopes. The production of his own microscopes seems to have been inspired by reading a copy of Robert Hookes book micrographia, where Robert Hooke had illustrated pictures of fruiting structures of common molds in 1665. He would go on to produce over 500 microscopes, though only a few survive to this day (sadly) and are comparatively rather simple being powerful magnifying glasses as compared to the complex compound microscopes used today*.

A portrait of Antony van Leeuwenhoek (left) and one of the simple microscopes that he produced (right).

In order to get a good view of what he was looking at using these microscopes he had to spend a considerable amount of time fiddling with various settings and a lot of patience. In the end he did in fact succeed and with the help of a hired artist, described and had drawings done of many of the small structures he could analyse with his microscope. In 1673 he began to write letters to the newly formed Royal Society of London and one of the first things he sent was a letter detailing the structure of a bees stinger. Over the next fifty years, he would have quite a large amount of correspondence with the Royal Society, who would translate his letters from Dutch and publish them in Latin or English. He would go on to analyse a large number of structures, such as the gills of an eel, but from my point of view by far the most interesting things that he described were unicellular organisms.

For example he discovered a great number of protists, including Vorticella a cilliate that can be found in pond water and has a taste for bacteria. By far one of his most important discoveries and rather remarkable given the primitive microscopes he had available, was his discovery of bacteria in 1676 while analysing pepper-water infusions. Unknown to him at the time as bacteria, he drew many of them and published the findings with the Royal Society of London calling them “wee animalcules”**. His original drawings contain many of the basic forms that bacteria take, including spirochetes, cocci (spherical) and rod shapes (noting that the links are all to modern images, I couldn’t find a readily available picture of van Leeuwenhoeks original drawings). While his observations of bacteria and other microorganisms were confirmed by others later down the track, it took a considerable amount of time (over 150 years) for the significance of these ‘wee animacules’ to be truly understood by the scientific community. None the less, Antoni van Leeuwenhoek was a truly remarkable man and continued his observations all the way until his death in 1723, setting important groundwork for later microbiologists to follow.

*It’s worth noting that compound microscopes did exist during his day, but these were very difficult to produce and were not as effective as todays, only being able to magnify things up to 20 or 30x.

**I am aware he spelt it “Animalcules” and this blog does not incorporate the other L. Oh dear. There is a highly compelling and extremely satisfying answer to this question as to why I forgot the other L. I am just not sure what it is.

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