With what does science deal?

Why, reality, of course.

If that seems like a simple answer, it’s because the answer is simple. We could break everything down, get more particular, explore general concepts, use specific examples, etc. That would give us a better understanding of how science works, but the answer to the question of with what it is science deals is the same: reality. Unfortunately, not everyone understands this:

Science is great for material things, but by definition it doesn’t deal with immaterial things.

This comes from our friend Neil. I usually reserve him for use in my “Punching Bags” series, but I’m actually still trawling his comment section to find more unique bloggers (not to mention bloggers who actually dare to defend their positions). As a result, I’m not particularly reading his writing – in fact, I’m not going to bother reading the rest of his post – but the above comment did catch my eye. It represents a weak mind.

Making the point that science only deals with material things, not immaterial things, is like saying science only deals with material things, not unicorns. It’s a meaningless statement. Unless, that is, Neil has provided evidence for the immaterial. But wait! Then he would have to use the material world and thus science. Since, by definition, he cannot use these things to study the immaterial (or unicorns), his views are fundamentally anti-science. In fact, the same goes for absolutely anyone who believes in the supernatural. It’s just kooky thinking.

Gay parents and appropriate science

I just read an article on why gay parents may be better parents, on average, than straight parents and I was reminded of some common abuses of science. These abuses were markedly absent; the article took the time to qualify what it was saying, calling speculation just that, pointing out when a point should be construed narrowly and not broadly, and generally being scientifically appropriate. Here is my favorite part:

The bottom line, [New York University sociologist Judith] Stacey said, is that people who say children need both a father and a mother in the home are misrepresenting the research, most of which compares children of single parents to children of married couples. Two good parents are better than one good parent, Stacey said, but one good parent is better than two bad parents. And gender seems to make no difference. While you do find broad differences between how men and women parent on average, she said, there is much more diversity within the genders than between them.

Emphasis added.

Most of the article is on a few studies and the reasoning behind their conclusions – gay parents tend to choose to become parents whereas straight parents do it by accident about half of the time – but I really liked this part. It is so often that bigots go around and misrepresent the data. They love to look at studies comparing X to Y and then extrapolate it all to Z without any justification at all. I would say it is purely an ideological thing, but when we’re talking about sexuality and religion is involved (as it is with the particular bigot to whom I linked), I suspect sexual insecurity is a huge factor as well. It’s sad.

I’m glad LiveScience took the time to show an appreciation for science.

Punching bags

I really don’t read Neil’s blog very often. I usually scoot over there for a peak when I’m writing a post for FTSOS and I need to reference an old post. Those old posts often have links back to Neil’s and so I take a glance. And what do I see every time? Something wildly wrong:

The explicit reason for both the junk DNA error and the vestigial organs error was the need to find evidence for Darwinism in the form of stuff in life forms that doesn’t work. Without that need, these errors would not have been made. For many kids, mid-twentieth century, it was an error that resulted in needless, risky surgeries, removing supposedly vestigial tonsils and adenoids.

Neil is quoting from Uncommon Descent, a creationist blog that demonstrates the same understanding of biology as Neil has – none. That’s why this is such an easy one.

First, most DNA still is junk, i.e., non-coding and without use. It’s largely unneeded and has no developmental use or phenotypic effect. What was once labeled “junk” may have regulatory business to go about, but that is not the majority of DNA. Deal with it, creationists.

Second, I can’t believe creationists are still confused about vestigial structures. It was never the argument that these structures used to have a function and now they don’t. The argument was – and is – that they evolved to have a particular function, but they have since lost that function. They may well have been co-opted into having other uses, but that is not important to whether or not they are vestigial. Uncommon Descent and Neil ought to be hugely embarrassed.

Third and finally, tonsils were historically taken out for a number of reasons. One reason has to do with the availability of medicine to treat inflammation. It wasn’t until the middle of the previous century that penicillin and erythromycin were put into wide-spread use. Without that treatment option, surgery was a very viable solution. Second, improvements in surgical techniques plus the 19th century discovery of anesthesia made surgery that much easier. Third, long-term statistics were not particularly available concerning the effectiveness of the surgery. It was clear that it improved a person’s well being in the short-term as far as inflammation and soar throats were concerned, but beyond that it was a bit of a mystery. What was clear was that it did not pose significant long-term risks. Finally, the practice of removing one’s tonsils dates back approximately 2800 years prior to Darwin. The procedure is not based upon evolutionary thinking, nor was it ever utilized in an attempt to justify any claims about the vestigial nature of tonsils.

This is getting to be too easy.

And an abuse of philisophy

Given my need to use a link within a recent post, I clicked over to Punching Bag Neil’s site. I found one of his traditional trolling Red Herring Theist posts where he says atheists have no grounding for atheism. Quoting another Red Herring Theist, he poses this question:

Here are some questions you can ask Richard Dawkins (and by extension any new atheist) the next time you sit next to him on a bus:…

• What makes your moral standard more than a subjective opinion or personal preference? What makes it truly binding or obligatory? Why can’t I just ignore it? Won’t our end be the same (death and the grave) either way?

I know Neil has this nasty habit of insulating himself from most outside criticism – it’s a common thing in the Christian blogosphere – but I would like to turn the question back on him and his silly little Christian brethren. What makes your moral standards more than subjective? How do you objectively know God exists? How do you objectively know anything in the Bible is true? Are you God himself? If not, then what method are you using to get outside yourself? After all, if you’re using a human brain to interpret anything, you can’t possibly be doing something which is not 100% subjective.

So why are you raising yourself to the level of God, Neil? Aren’t you being disrespectful to your particular, cultural icon?

More abuse of science

It’s a common tactic for anti-gay bigots to distort science. One of their favorites ways to do so is to find studies which are limited in their scope to ‘traditional’ families, but then they take a wrecking ball to the science by pretending that they’re looking at something comparative. I documented one bigot who did just that.

But that isn’t their only tactic. So long as they can distort a scientific study in some way, they will. Take this instance of an anti-gay bigot from the Congressional hearings on the repeal of DADT.

This is common not only of Christians, but much of the conservative movement. So long as a citation is being made, they think they’ve proven their case. Who cares if their source actually contradicts what they have to say?

Punching bags

Whenever creationists get hold of a legitimate scientific paper, I groan a little bit for at least two reasons. First, I know whatever they have to say, they’re going to mangle the science. We saw that with Jack Hudson last year (and, actually on literally every post about science he has ever made). And, of course, we also saw that with all the other creationist sites from which Jack stole his material. Second, I know I’m going to have to devote some time to reading and blogging on a paper I would have otherwise missed. It isn’t that I don’t like to read these things – I do. The problem is that it’s a time-suck when the blogging is factored in. You see, unlike creationists I actually research and verify what I have to say on any given piece of science.

Let’s start with the paper in question:

Here we report exceptionally preserved fossil eyes from the Early Cambrian (~515 million years ago) Emu Bay Shale of South Australia, revealing that some of the earliest arthropods possessed highly advanced compound eyes, each with over 3,000 large ommatidial lenses and a specialized ‘bright zone’. These are the oldest non-biomineralized eyes known in such detail, with preservation quality exceeding that found in the Burgess Shale and Chengjiang deposits. Non-biomineralized eyes of similar complexity are otherwise unknown until about 85 million years later6, 7. The arrangement and size of the lenses indicate that these eyes belonged to an active predator that was capable of seeing in low light. The eyes are more complex than those known from contemporaneous trilobites and are as advanced as those of many living forms. They provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology, and are consistent with the concept that the development of advanced vision helped to drive this great evolutionary event8.

The gist of the find is this. Researchers discovered very old fossils of arthropod eyes from the Early Cambrian. They do not predate complex eyes, but they do predate similar non-biomineralized eyes. That is, trilobite eyes are made of calcite, meaning the trilobites produce the minerals for their eyes themselves. In turn, their eyes are hardened (and thus more easily fossilized). So these new fossils show a different way in which eyes could become complex. Furthermore, they showed a tight packing in the lenses, much in the way that a fly’s lenses appear to be tightly packed. They also were curved to form binocular vision, meaning there was a visual overlap in front of the body. This helps for judging distances and discerning complicated backgrounds. This creature was a predator.

But here is where creationists draw issue:

Did you catch that? If you were a high school student who trusted your teachers, you’d think they had evidence for this unbelievably rapid amount of highly complex change. But they merely assume that it evolved, so it “had” to have been a great evolutionary event and another example of “rapid innovation.” [And is thus a tautology.]

This comes from Neil who, like many creationists, was taking his cue from another site. He believes that every paper that mentions evolution must provide a detailed description of why evolution is true.

His quote was a reference to this excerpt from the paper:

[The new fossils] provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology, and are consistent with the concept that the development of advanced vision helped to drive this great evolutionary event.

What this is referencing is the fact that until now advanced eye fossils were almost exclusively restricted to trilobites in the fossil record. These new fossils give evidence that, as suspected, there were other marine creatures swimming around with complex eyes. Furthermore, they show a quantitative change in the number of lenses, not the sudden appearance of these sort of lenses. (But note that we can’t expect to see a perfect fossil record. We can get a good outline, but it’s silly and really very ignorant for creationists to demand to see every intermediate organism. At some point things will have to “suddenly” appear. Of course, this is in geological terms, i.e., over millions of years.) These eyes are evidence that evolution was driven in part by the anatomical changes in vision during the Cambrian.

So it is clear that none of this is a tautology. This fossil find is further evidence of the nature of evolution and the role vision played in its creation of arms races. What we see from the creationist world, however, is an immature understanding of the science. There is no doubt that Neil never bothered to read the paper from Nature, nor have many of his creationist brethren. If any of these sort of non-academics bothered to look into the literature (or even take formal courses), they would see their obvious errors. Further, even if we are to understand this paper as Neil purports it to be, he’s still in error. That is, he believes the paper is a tautology because it assumes evolution without giving evidence for why evolution is true. This is like drawing issue with physics papers because they assume gravity is true without explaining general relativity. It’s a silly complaint to make and it only demonstrates how wildly over the head of creationists most scientific papers are.

Proven right in mere hours

It was only a few hours ago that I wrote about the condescension being expressed towards women who decide to have an abortion. The Republicans just don’t get it. Women aren’t getting abortions because they haven’t seen their ultrasounds. They aren’t making these decisions lightly. In short, women are not stupid. It’s crazy, I know. But one pseudo-libertarian right winger wants to make sure you all know I wasn’t just creating a strawman:

The pro-choice lobby has spread so much anti-science garbage over the years, I don’t for a minute believe that most women realize the implication of their decision to abort. Not for a minute.

Well, I never did expect someone from the right to believe in facts. Not for a minute.

The majority of the rest of this guy’s post is just projection – he knows the right has no grounds for claiming the side of science in anything, and he knows the entire point of all the ultrasound laws being proposed or passed in recent months is to be emotionally manipulative – plus he has a healthy does of red herring in there, but I am interested in one thing he said:

There is no debating that unborn children are human beings. Period. Science is clear on this issue. So, why are you being so anti-science by hinting toward a philosophical argument?

This reminds me so much of Punching Bag Neil. “Science is clear! Humanity begins at conception!” Except it doesn’t. What starts at conception is a process of development. Where that development starts to matter is a complicated issue – so complicated, in fact, that we can’t really begin to talk about it when people on the right don’t even understand the basic biology behind the issue.

Update: I noticed that one key part of my post wasn’t reposted by this guy. It was this picture showing the breakdown of what Planned Parenthood does. It shows that only 3% of their services are directed towards abortions. But do these facts matter? Of course not!

Why can’t you people just admit the facts? Why can’t you admit that Planned Parenthood’s livelihood is abortion services? Why can’t you people just admit that the trumpeted Hyde Amendment is utterly meaningless, because money is fungible!

Support abortion if you so choose, but for God’s sake, quit lying!

So when the facts are inconvenient, the other side is lying. Got it.

Punching bags

Once again Neil has proved a great resource for punching bags. Following the link to one of his commenter’s blogs, I found this link to Cornelius Hunter. The guy has written an anti-science book or two and works for – you guessed it – the anti-science Discovery Institute. He has a post about convergent evolution, something he doesn’t appear to understand.

Imagine a future space explorer who travels to a distant galaxy and discovers an inhabited planet with an advanced civilization. In his visit he tours a great art museum. The halls are adorned with many beautiful paintings, but as the traveler walks through the museum an eerie feeling of deja vu overtakes him. The various exhibits he observes show different styles and movements that are uncannily similar to what he is familiar with from his home planet. Even particular paintings are incredibly similar to what he remembers.

Ergo, God.

But despite making his entire argument, and roughly half of the arguments from the Discovery Institute, Hunter continues.

This would be eerie because this high similarity has occurred for no apparent reason.

Well, gosh, he surely can’t be implying that convergent evolution happens for no apparent reason, can he? Because we do know that similar environments are a major cause. When two distantly related species which do not share a (recent) common ancestor are each in a similar environment with a similar niche to fill, they may both well fill it. Hunter may as well be saying that evolution itself happens for no apparent reason. We either know or can infer the reasons behind why many traits evolve. That they sometimes evolve independently and then converge does not throw the world of evolution on its head.

A million different paintings are possible, the traveler would never expect to see such similarity in independent masterpieces.

Except Earth doesn’t have a million different environments, broadly-speaking. And life has been around for 4 billion years. And not every option is equally viable. The odds, it turns out, really aren’t so bad. At least, ya know, when we feel like using facts and junk.

The level of convergence in biology has been found to be amazing in recent decades. Strikingly similar designs run all through the biological world. Such similarities do not bode well for evolution because (i) they are supposed to be independently created by chance events,

Chance? Nope. Wrong. They are created via nonrandom natural selection acting on populations that usually exist in similar environments and therefore have similar needs and/or possible outcomes.

(ii) often they must have arisen in different initial conditions,

The foundation of biology isn’t turned on its head because organisms use a different starting point. In fact, we ought to expect many different starting conditions; we see different biochemical pathways, different genes, and even different (sometimes subtle) morphology which all indicate differing evolutionary histories. That these pathways converge is indicative of patterns in the way life operates, not of the Jesus answer Hunter wants. Indeed, instead of Hunter’s anti-science response of “Nuh-uh, couldn’ta happen’d!”, we have some very interesting questions raised through ever-increasing discovery.

(iii) often they are found in different environments

So? Similar environment is the big cause, but that doesn’t make it the only cause.

(iv) the design space is large

This is just a repeat of his analogy. It’s still wrong.

How can we understand these strikingly similar masterpieces?

Well it really isn’t so difficult after all. You see, if our eye evolved once, then why not twice? Evolution is a story of serendipity, so why not add a bit more? Accepting the evolution of life requires a credulous mind. Once evolution is accepted as fact, all kind of events can be accommodated.

In other words, convergent evolution proves Jesus because it’s really hard to understand. If that’s the case, then I think Jesus is proven to Hunter all the time. Also, convergent evolution is false because, um, uh, ’cause things can’t convergently evolve.

Consider how evolutionist Simon Conway Morris explains convergence at the Map of Life website that documents convergences. Incredibly, for Morris, not only is convergence not a problem for evolution, it actually is yet another proof text. The message from biology’s massive convergence is “First, that evolution is true.”

First, Hunter doesn’t link to any explanation of convergence. He links to the page that describes the aims of Morris’ website. Second, it is the message of the website that evolution is true, not of convergent evolution. Call me crazy, but if a theory can be said to have a message, I would say convergent evolution’s message is that, in evolution, convergence happens. But maybe I’m just being wacky.

And how do these convergences help support such an amazing conclusion? Morris explains that biology’s very complex structures, such as the bacterial flagellar motor, “evolved independently at least twice.”

In other words, if you think complexity argues against evolution, just look—convergence reveals independent versions, which of course must have evolved. Such independent evolution proves such structures can’t be too complex.

…what? Convergent evolution doesn’t mean that something is therefore simple (though a strong case has been made for Hunter’s simplicity). Very complex structures or characteristics or traits can come about through evolution while landing on a similar spot or the same spot. Hunter’s conclusion has no relation to anything any real biologist has ever said.

Next please.

Punching bags

I want to start a new series, but I need your help.

There are bloggers and other individuals out there that just offer themselves up as punching bags. They are always antiscience. But I can’t find them all. For instance, my most recent punching bag, Neil, only came across my radar because of how wildly confused he is between the science of development and the subjectivity of “humanity”. Not everyone is that blatant in their misunderstanding of basic science. (Okay, so every single creationist is that blatantly confused, but I want to find some people more worthy of my time.)

So I’m not looking for people who raise legitimate scientific questions; I’m not about to get into a match with Jerry Coyne over how to define “species” (especially since I generally agree with him anyway). I want punching bags: people who mangle legitimate science for the sake of their point of view – a point of view they formed independently of anything to do with science. Alt-med quacks are always good, though creationists will work when the issue is topical, i.e., new hot-topic research. I don’t want the big names like Chopra for this series, but don’t be afraid to send me that sort of malarkey as well.

If you find something you think would fit these posts you can either make a post right here or email me at forthesakeofscience@gmail.com. Just be on the outlook for buzzwords like “quantum” or for people who draw nebulous connections between real studies and their worldview. Those people make up the most solid candidates.

The abuse of science

We see creationists distort science all the time. They usually do it when the topic is something they really don’t understand; they’re driven by an ugly agenda. Sometimes that agenda is to explicitly undermine real science. Other times it’s to abuse science. This post is about an instance of a creationist engaging in that abuse.

New study links father absence to increased bullying – so when people want to reduce bullying in schools across the board – instead of just protecting their favored students – remind them how important stable one man / one woman families are.

This comes from Neil, that religious nutbag who doesn’t know the difference between the scientific concept of development and his subjective declaration of “humanity”. Committing the same error as his source, he draws inappropriate conclusions from the study. Fortunately yours truly is here. As someone who isn’t interested in distorting science for my own gains, let me explain what the study actually said.

This research investigates the relationships among bullying behavior, mother’s and father’s work hours, and early adolescents’ perceptions of whether they spend sufficient time with their parents. In cross-sectional models, we find maternal work hours are modestly associated with increases in bullying behavior. However, in more rigorous change models, our findings indicate that over time maternal work hours bear no direct relationship to bullying behavior. Moreover, in our final models, an interaction between father’s work hours and perceptions of time spent with him has one of the most robust associations with bullying for adolescents. When paternal employment is full- or overtime and youth perceive they do not spend enough with their fathers, bullying behavior increases. Other important factors that shape bullying behavior are the quality of the home environment and the adolescent’s school performance.

That’s just the abstract; the rest is behind a paywall. More information can be found in the ScienceDaily article.

Basically what the study showed was that when kids had their fathers around, they were less likely to be dicks. Great. What the study didn’t do was compare children of gay couples who had both parents around. It is logically, scientifically, and morally inappropriate to conclude that same-sex marriages produce kids who tend to bully more. We have no evidence even suggesting as much.

It really bothers me when people take these sort of studies and then try and use them to denigrate gay marriage. It isn’t that the bigotry behind it all is frustrating – though it is. It’s that, hey look, we have this scientific study here that was done by a lot of hard-working people with a lot of experience and knowledge, their methods are good, the conclusions are interesting, and there are some clear things we can draw from it all. But then there are these anti-scientific, lazy people with no experience or relevant knowledge, no understanding or appreciation of the methods used, and they aren’t interested in the conclusions at all; it’s all about abusing the science for some petty point, a point that isn’t even on the right side of history.

I’m all for applying our scientific knowledge in how we run ourselves as a society, how we consider our worldviews. I just don’t want to see it all get abused for political points. That’s what happened to this study. It’s unfortunate. We have this serious issue of bullying being considered by a group of serious individuals, and we have these good results that tell us kids are more well adjusted in a particular category when they perceive their fathers, married and heterosexual, as being around more, but then someone has to come around and piss all over everything. All we know from this research is what is says about kids with married, heterosexual parents versus other kids with married, heterosexual parents. Claiming it tells us something different or more is an abuse of science.