Autism & Vaccines Revisted (... again)

Tuesday, June 30, 2009 at 12:39 PM Bookmark and Share
Massimo Pigliucci's has a nice post on his blog Rationally Speaking, summarizing a recent eSkeptic article entitled "Vaccines & Autism: A Deadly Manufactroversy." It's a nice read for those unfamiliar with the history of the widespread fear that vaccines are the cause of autism, and the consequences of that belief.

In case you're wondering "Why all the fuss about the 'vaccines cause autism' scare?" I think the issue warrants attention for at least two reason: First, as countless individuals and organizations have made abundantly clear, we need vaccines to prevent the death and life-long suffering caused by preventable infectious diseases, particularly among children. Second, we need to focus on uncovering the real story behind autism so that we can more effectively treat and prevent autism spectrum disorders.


Quinn, a boy with autism, and the line of toys he made before falling asleep.
More about Quinn at: http://www.youtube.com/watch?v=G7kHSOgauhg



A boy with a rash indicative of rubella (German measles)
(click and search the CDC images for "10146" for details).
Rubella during pregnancy can cause severe birth defects.


Lizard tales from the world of science and engineering

Thursday, June 25, 2009 at 9:08 PM Bookmark and Share

I occasionally check TED.com for any interesting new talks, and today I came across a pretty cool one by biologist Robert Full, on what we are learning about geckos from attempts to mimic their legendary climbing abilities. Here's a link to the talk (with a link to download or watch a high definition mp4 version):
Robert Full:
Learning from the gecko's tail
Geckos in wind tunnels, snazzy biomimetic robots, rock climbing, multidisciplinary approaches to doing science - it's bound to be well worth 10 minutes of your time! ;)


The Origin of Species: Creationism Edition

Tuesday, June 23, 2009 at 8:46 PM Bookmark and Share
That's right - "Origin of Species - Containing the Gospel and Intelligent Design" - coming to a bookstore near you!

What's so special about this edition? Well, for one, the special introduction by Ray Comfort - world renown science buff and public educator extraordinaire creationist and fumbler of basic concepts in science. Fortunately, you don't need to pay anyone money to read this gem of science evangelical writing, as the introduction is linked from the page above.

In case you don't know who Ray Comfort is, he's perhaps best known for his Christian evangelism along side Kirk Cameron, and of course this stunning display of his deep scientific knowledge...



Still curious?? Well, for a really well done treatment on the efforts of Comfort and Cameron, check these three videos:







As for the 50 page "Special Introduction" (here) to Darwin's Origin - lets take a peek, shall we?

Now, I'm not going to dissect and correct the whole thing - that's simply a waste of my time, and I'm sure others will do a good job of this in the coming days and weeks (I'll post links below).

Instead, I'll just point out a few things and leave you to look around and do a little follow-up of your own using the many freely available resources on science and creationism, as TalkOrigins, youtube, and whatever you can dig up using google.

I have to confess that it's truly amazing to me how these guys repeat the same old fallacious arguments and factually incorrect statements - the exact same ones they and other creationists have been ridiculed for time and time again... At the heart of much if it, you can see and hear what appear to be a serious lack of understanding about basic science and logic, and a clear attempt to attack the theory of evolution in an effort to promote their own religious agenda.

For example (from page 9)...
The DNA Code
Consider for a moment whether you could ever believe this publication happened by accident. Here’s the argument: There was nothing. Then paper appeared, and ink fell from nowhere onto the flat sheets and shaped itself into perfectly formed letters of the English alphabet...
etc. etc. etc. then
Do you think that DNA’s amazing structure could have come together by accident? Or does it point to an intelligent Designer? Even the director of the U.S. National Human Genome Research Institute concluded there is a God based on his study of DNA. Francis Collins, the scientist who led the team that cracked the human genome, believes...
This is a classic goof - the notion that evolution asserts life or all of existence just all fell together by some sort of "accident" - this is a big red flag! It suggests that the author (1) has a horribly incorrect understanding of evolution, other natural sciences, etc. or (2) they're simply disingenuous and out to bend the truth. I'm not sure if Comfort falls into either category, but given the availability of these critiques one really does wonder. Add to that the assumed designer (bet you can guess who that is?) and an appeal to authority to top it all off, and your B.S. detectors should be blazing off the charts!

In addition to these sorts of nonsensical arguments, the terminology used also indicates a frightening lack of science literacy:
DNA is an incredibly detailed language, revealing vast amounts of information encoded in each and every living cell — which could not have arisen by accidental, mindless chance.
Still - they do make a good point. It would take something like - oh, I don't know - natural selection to explain it all? We'll be really nice and pretend this was the author correcting the egregious mistake I just pointed out above... moving on.

This document contains a number of other questionable assertions and logical errors. For example, consider the statement that "Information requires intelligence and design requires a designer." The first - nonsense! The second? Well, yeah, of course - by definition! So what's the point of stating the obvious? Well, lets just say it helps explain some of the examples we're about to have thrown at us.

One such example requiring these fuzzy associations is the bit involving Mt. Rushmore. Another classic example creationists use - this one being the argument from design. When you cut through all the fuzzy wording, you see that the argument in this case goes something like this: things designed by people are designed by people (e.g. Mt. Rushmore), therefore complicated stuff (e.g. eyes, flying insects, etc.) is designed by the only possible designer, God.

Oh, Darwin would be so honored to have such a fantastic introduction to his most famous work!

The introduction also gets into one of my favorite creationist goofs... rationalizing genetic evidence supporting evolution and refuting a literal interpretation of Genesis. Why do I love this one so much? Because it highlights the importance of both science and history!

Perhaps not surprisingly, folks who manage to botch basic science also frequently fail to grasp some important aspects of relevant history. In this case, that bit of history is what all this genetic evidence really means to the claims of creationists over the past century or so.

Here Comfort brings up a typical example: the genetic similarity between humans and chimps (although we could also apply the following to the scientific hypothesis-turned-theory that all life shares a common ancestor that lived a few billion years ago).

During Darwin's later years towards the end of the 1800s, when (at worst) all we had was morphological data from living organisms and some weak fossil evidence supporting the theory of evolution, creationists of the day were very vocal about the notion of having primate ancestors... they would have none of it! Then, just decades ago, the discovery of DNA leads to an explosion of genetics research, and from it we discover a huge and growing body of evidence that confirms the predictions of evolutionary theory including common descent with modification by natural selection. Add to that the boom in fossil discoveries since Darwon's day (yes, plenty of intermediate forms - just as predicted by evolutionary theory) and the evidence is really overwhelming.

So what's a creationist to do? Follow the fringes of science, and let the rationalizations begin. Did we evolve from apes? Why all the physical, behavioral, and genetic similarities? Comfort, of course, has the answer:
When you see a biplane and a jet—which share common features of wings, body, tires, engine, controls, etc.—do you assume that one must have evolved from the other naturally, without a maker? That’s illogical. It’s more reasonable to conclude that similar design indicates a common, intelligent designer. An architect typically uses the same building materials for numerous buildings, and a car manufacturer commonly uses the same parts in various models. So if we have a common Designer, we would expect to find that a similar “blueprint” was used in many different creatures.
See, so if we just recognize that there was a designer, then clearly this is all just proof that there was a designer! So simple! Yet, unfortunately for Comfort, so wrong. You see, again we have the problem with the design argument - if you prove it by assuming it, you haven't really done much, now have you?

Interestingly, Comfort also doesn't appear to have actually taken the time to learn the science he's trying to debunk, and as a consequence he ends up making a fool of himself and his cause in the minds of knowledgeable people who see gaping holes in his competence. For yet another example check pages 13-14 for a little more of Ray's (mis-)interpretation of the science:
After all, DNA is the coding for the way our bodies look and operate, so creatures with similar features or body functions (eyes for vision, enzymes for digestion, etc.) would have similar coding for these things in their DNA.
Err... nope, not quite. In this case, counterexamples are easy... form and function do NOT imply genetics - it's the other way around! For such examples, see the many cases of convergent evolution, the fact that eyes have evolved in many different ways in different organisms, and so on.

Indeed, the list goes on and on... like shooting fish in a barrel.
If evolution were true, and humans and chimps did have a common ancestor, we would expect to find something that is half-monkey/half-man. These intermediate stages where one species supposedly evolves into another species are called “transitional forms."
Yes, he botched evolution again, I know, but he's onto something! Is he suggesting we look for empirical evidence of our primate ancestry?? Here, Comfort digs himself yet another hole since we have those fossils - lots of such fossils, in fact. In addition, as mentioned above, we've also got the genetic and morphological evidence too. Fortunately for Ray, he might still be able to try the old creationist trick of simply demanding transitional forms for all the transitional forms and more and more such evidence - so he's safely guaranteed to NEVER be sufficiently convinced of anything.

And with that, I'll wrap it up and leave you with a few links. I'll add more links as they become available, but feel free to share anything else in the comments below.

-------------------------

For more on evolution and fossils:
1. Don Prothero's book "Evolution: What the Fossils Say and Why It Matters"
2. I hear Jerry Coyne's book "Why Evolution is True" is also quite good.
3. The www.talkorigins.org archive.
4. PNAS has made 19 papers freely available as a supplement to the 16 June 2009 issue:
Supplement to the Proceedings of the National Academy of Sciences of the United States of America, which includes articles from the Arthur M. Sackler Colloquium of the National Academy of Sciences In the Light of Evolution III: Two Centuries of Darwin. The complete program is available on the NAS web site at www.nasonline.org/sackler_darwin
More on Ray Comfort & The Origin of Species:
1. Special Origin of Species to be Given Away in Schools
2. Original post at the blog Pharyngula.
3. Ray Comfort's Wikipedia entry.

-------------------------

The Letters To Our Daughters Project

Saturday, June 20, 2009 at 11:36 PM Bookmark and Share

Back in early May, I posted about the Letters to Our Daughters Project that was launched by Isis the Scientist. The goal is to invite senior female scientists share some of their experiences and wisdom with the next generation of female scientists. So far, they've done a brilliant job of it.

The letters are all be available to read by clicking here. Give'em a read, share them with the young scientists, and check back for updates!

God exists - Q.E.D.

Wednesday, June 17, 2009 at 2:58 PM Bookmark and Share
Back in April, I made a post entitled "Can you recognize a flawed argument when you hear one?", and today, I came across yet another opportunity to ponder another bad argument (again, from the blog Sandwalk).

So here's the example that prompted this post (and another couple of essays to hopefully balance things out - whether you believe in God or not). First, check out Proof that God Exists and see if you can nail down where their argument gets shaky, what additional assumptions are implicitly made, etc.

At the other end of the spectrum, a good many atheists are pretty well convinced that "there is not God." So here's another line of arguments to try and pick apart. See what you come up with from the essays entitled "God Doesn’t Exist, Part II - Arguments against the Existence of Gods" and if you'd like, "God Doesn't Exist, Part I - Proofs of the Existence of a God."

Whatever your beliefs, keeping your B.S. detector sharp is a good idea. If someone comes up to you and says "I can prove that 2+3=4!" you might be inclined to entertain them (and yourself) and hear out their argument. Still, you're pretty sure they're about to utter some particular flavor of bad arithmetic, and no doubt you'll be extra alert just waiting to pounce on their seemingly inevitable mistake(s). As any good elementary school math teacher would agree - it isn't always important whether or not they get the right answer, but often it's whether or not they know how to get the right answer. Which is good enough reason for me to try and exercise my logic muscles a little bit from time to time. ;)

So imagine someone comes up to you and says "I can prove that 2+3=5!"? You might think, "well, yeah - me too!" and not even bother to hear their proof. After all, you're darn well sure that they're right! Even if you do give their argument a listen, are you as eagerly listening for mistakes or are you perhaps a bit tuned out and just going along for what you expect to be a straightforward argument? Maybe arguments for what we already believe to be true don't quite get the proper level of criticism they might deserve? (Gasp!)

This is presumably a pretty well known behavior (I'm almost certain that philosophers and/or psychologists have a name for it?). Still, it's worth remembering if we're going to try and keep from getting duped or from becoming overly certain of our own unfounded beliefs - be they on one side of the fence or the other.

Ever used a homeopathic remedy?

Tuesday, June 16, 2009 at 8:57 PM Bookmark and Share
Surprisingly, you may have - and not even known it.

Some over the counter pills and sprays are homeopathic preparations (that is, some focal ingredient that has been diluted down to only a few molecules - or likely none at all), combined with other filler materials and usually some "vitamins or minerals". While labeled as homeopathic, as required by law, some folks simply overlook these details or fail to grasp what "homeopathic" really means.

I myself used one once - a free sample of Zicam I received as part of a complementary box of toiletries or some sort of product sampler I picked up somewhere (it was a while ago). So why did I try it despite my strong suspicion that it would have no impact on my symptoms? Simple - it's homeopathic! There's nothing in it but some pill-fill and vitamins! What's the harm!?

Well, as it turns out that question sometimes has some unexpected answers. There's actually a site called "What's the Harm?" that is chock full of the dangers of complementary and alternative medicines like homeopathic remedies, though it should be mentioned that anecdotal evidence is not nearly as compelling as the kind of evidence we can get from large well controlled studies or decent statistics based on reliable public health data.

Today, the FDA added more to the list: Zicam Cold Remedy Nasal Gel, Gel Swabs, and Kids Size Swabs. According to reports, Zicam users may suffer anosmia - the inability to percieve smells. A quick google seach of "Zicam FDA" turns up plenty of news briefs on the matter.

So aren't these things regulated by the FDA?? Well, actually, they're hardly regulated like real drugs other remedies.
[T]he FDA treats homeopathic remedies very differently from conventional medicines. Homeopathic products do not need FDA approval before sale; they do have to be proven safe per the Dietary Supplement Health and Education Act of 1994, and they do not have to prove efficacy. Homeopathic remedies do not have to be labeled with an expiration date, and they do not have to undergo finished product testing to verify contents and strength.
Hmmm...

To be fair, the FDA doesn't have any smoking guns - just lots of suggestive anecdotal evidence. Right? Well, there's more to it than that. You see, unlike the shaky foundation of homeopathy, we do have some good science-based understanding of what may be going on here: Too much zinc exposure can reportedly damage nerve function in the nose.

For other details, the FDA press release can be found here, with more details here. For the another perspective, here's what the company website has to say about the matter:
Message to Consumers
June 16, 2009

Matrixx Initiatives confirms that it has received a warning letter from the U.S. Food and Drug Administration about three of its 19 Zicam products, specifically Zicam Cold Remedy Nasal Gel, Zicam Cold Remedy Swabs and Zicam Cold Remedy Swabs, Kids Size, based on allegations that their use could cause a temporary or permanent loss of smell, known as anosmia. Zicam Cold Remedy oral products were not included in the letter.

Matrixx Initiatives' primary concern is consumer saftey. Based on the FDA's action, the company has suspended shipments of these products and will reimburse any customer desiring a refund.

However, the company believes the cumulative body of independent scientific and medical evidence supports both the safety and efficacy of Zicam intranasal cold remedy products. Matrixx Initiatives stands behind the science of its products and its belief that there is no causal link between its intranasal gel products and anosmia. For this reason, Matrixx Initiatives believes that the FDA action is unwarranted and will seek a meeting with the FDA to review the company's product safety data.

Evolution 2009 Conference

Monday, June 15, 2009 at 1:13 AM Bookmark and Share
Academic disciplines all have their big conferences, and this week a good number of biologists are attending Evolution 2009 hosted by the University of Idaho.



While I'm here at home working on thesis research instead of attending the conference, I'm going to try to catch some of the highlights of the meeting each day. How? Why, the internets, of course! ;)

For starters, there's the Evolution 2009 blog coverage page on the conference webpage. Already, there are links to photos from a pre-conference hike (err...), a cool discussion of how predation by snail-eating snakes seems to impose selection on a snail's favoring shells that spiral left instead of right, SJ Gould Award winner Eugenie Scott's lecture, and a few others.

There's also a schedule if you'd like to take the time and wade through it for any eye catching titles worthy of googling the author. While this usually isn't all that productive -- and not at all as informative as hearing some of the talks -- it can on occasion be fruitful!

For example, today I found this great little quote from Jeremy Fox's webpage, which I'm sure I'll use in future talks motivating biology students to become competent quantitative scientists:
I use mathematical models because ecology and evolution are complicated; it's impossible to develop rigorous hypotheses without mathematical help.

- Jeremy Fox, Biologist
Hey, give me break, I'm an applied mathematician - hearing biologists say things like this puts a big nerdy smile on my face!

Moving along, there's also the FriendFeed page which takes a bit more wading through tweets and other posts on such intellectually stimulating topics as where to get the best coffee or beer near campus. Eventually though, you can find some of the more interesting "tweets" like this one
visit the Systematic Biology exhibit for an amazing (free) Timetree of Life poster #E09
Which presumably refers to this poster (which is also available free to download from the web) from the TimeTree website.
Here's an example from this site, which attempts to give you estimates of the time since two given taxa diverged. I thought I'd check it out with an easy one (chimps and humans) - here's part of the result:


The TimeTree project has also gotten some attention at the phylogenetics blog dechronization - check it out!

Ah, now if the Evolution 2009 organizers had only recorded all the talks and made them available on the web...

That reminds me, I should post something about the recent Computational Sustainability conference last week at Cornell. Unlike the big conferences like Evolution, this one was a bit smaller and the organizers were kind enough to actually record almost all of the talks and put them on the web!!! I'll probably post more later, but for now here's a link to the webpage:
http://www.computational-sustainability.org/compsust09/
Videos of the talks are linked from the schedule.

The Placebo Effect

Saturday, June 13, 2009 at 3:20 PM Bookmark and Share
Following up on my recent post about recent research into "alternative medicine", I just came across this nice article from skeptic.com about the placebo effect. I found it well worth the read!

The secret life of the Long-beaked Echidna

Thursday, June 11, 2009 at 9:38 PM Bookmark and Share
As most of us learned in school, mammals all have hair and feed their young with milk-producing mammary glands. Most of us also learned about such crazy looking creatures as the egg-laying, bill-wearing, venomous oddity the platypus. Platypuses and their relatives the echidnas sport a mishmash of mammalian, reptilian and bird-like characters (and genetics!) making them pretty darn cool to most anyone interested in biology and evolution.

Amazingly, despite there being only a handful of echidna and platypus species living in the world, some of them are woefully understudied. Fortunately, some researchers are taking on the challenges of studying these animals, and as a result we're beginning to unravel some of the mystery surrounding these amazing little critters.

Before pointing you towards a nice article summarizing recent work on the Eastern Long-beaked Echidna, a quick refresher on mammalian taxonomy. Within the class mammalia, organisms are usually divided into two major groups: (1) the subclass theria which includes most mammals and is itself divided into two infraclasses -- the eutherians ("placentals") and the metatherians (marsupials and their relatives) -- and (2) the subclass protheria which is comprised of the single order monotremata - the egg-laying echidnas and platypuses (more on mammal taxonomy here). That means you yourself are probably more closely related to any random mammal alive on the planet today (whales, elephants, aye-ayes, bats, chimps, etc.) than you are to the echidnas or the platypus. But, I digress... time to get on to the article.

Today, an acquaintence of mine and professor shared this article (I'll admit it - it was via facebook) about the Eastern Long-beaked Echidna that summarizes some of the recent work published in the Journal of Mammalogy. The scientific article requires a subscription - or friend at a subscribing institution - to download:
Muse D. Opiang. 2009. Home Ranges, Movement, and Den Use in Long-Beaked Echidnas, Zaglossus Bartoni, from Papua New Guinea. Journal of Mammalogy 90(2):340-346. doi: 10.1644/08-MAMM-A-108.1
More on the article can be found over on Jerry Coyne's blog Why Evolution is True. More about monotremes can be found here.

What does science say about "alternative medicine"?

 at 11:07 AM Bookmark and Share
According to this AP article, it says that it largely doesn't work. Well, at least not any better than placebo. So if you think that herbal tea helps cure your colds, or that acupuncture can fix your intestinal problems, read no further!!!

While there have been some marginal successes, "it doesn't really work" is largely the take home message of the past decade of research findings coming out of the National Center for Complimentary and Alternative Medicine (NCCAM), an NIH program established in 1991 to investigate the claims of scientifically unproven methods for treating health problems - usually referred to as the more pleasant sounding "alternative medicine" - such as homeopathy, acupuncture, herbal remedies and other common alternatives to science-based medical treatment.

Some may argue that a lot of these efforts were (and continue to be) a waste of time and money. After all, I'm personally not all that thrilled to know that
...the government also is funding studies of purported energy fields, distance healing and other approaches that have little if any biological plausibility or scientific evidence.
Fortunately, not all of these studies dealt with claims that demanded such a stretch of the imagination. Other studies looked into more plausible claims,
Echinacea for colds. Ginkgo biloba for memory. Glucosamine and chondroitin for arthritis. Black cohosh for menopausal hot flashes. Saw palmetto for prostate problems. Shark cartilage for cancer.
and did so using methods that puts these "alternatives" on the same level of comparison with standard science-based medical treatments. Unfortunately (though not surprisingly), almost all of these "treatments" worked no better than placebos.

Whether or not these findings are worth the more than $2billion spent on the projects, I for one am glad to see some of these claims taken seriously, studied, and the findings shared with the public. To elaborate on comments made by NCCAM director Josephine Briggs at the end of the AP article, there's nothing wrong with building sound, science-based knowledge about these mostly ineffective alternatives, and sharing that information with the public so they can make well informed decisions about their health and the health of their families.

It does beg one question though... Can we "have our cake and eat it too" when it comes to reaping the benefits of the placebo effect while at the same time denouncing these treatments as ineffective? Seems like a slippery slope to promote some of these alternatives on this basis, but still an interesting question.