Archive for February, 2009

Chemists as creationists: A formula for disaster

Friday, February 20th, 2009

A colleague in the natural sciences department here at the college handed me a printed copy of an article recently, and asked me for my opinion “as a chemist” on it.  I took the article and, since it was about 2 minutes before my next class, said I’d look at it later.  Later came, and I was in for a bit of a shock.  The article in question was one from the “Institute for Creation Research”: Chemistry by Chance: A Formula for Non-Life by one Charles McCombs, Ph.D.

Dr. McCombs seems to be a retired organic chemist.  So, you would expect McCombs to have some chemical objections to evolution.  (As commenter wb points out below, he is really trying to critique abiogenesis – what happened before evolution started.)

Before we get started, I’d like to point out the format of the article.  It’s a list.  Like many creationists, McCombs spews out a bunch of soundbite-sized objections to the science in the hopes that something will stick.  Most of these objections are simply old creationist claims that have been debunked a hundred times over.  You can read about those – like [the stability of biomolecules] and [the “problem” of chirality] – over at the Index to Creationist Claims.  Let’s see what McCombs says that might be new.

In a watery environment, amino acids and nucleotides cannot combine to form the polymeric backbone required for proteins and DNA/RNA.

Never mind, of course, that living cells do this sort of thing, and they’re 70% water.

In the laboratory, the only way to cause a reaction to form a polymer is to have the chemical components activated and then placed in a reactive environment. The process must be completely water-free, since the activated compounds would react with water. How could proteins and DNA/RNA be formed in some primordial, watery soup if the natural components are unreactive and if the necessary activated components cannot exist in water?

The way we choose to make a chemical in a laboratory environment may be quite different from the way a chemical can be made in the natural environment. I may choose to make oxygen gas in my lab via decomposition of mercuric oxide, but that’s not how the algae in the pond across campus do it.

Since living cells can manage making peptides with water around, you might envision that there would be some mechanisms available for the formation of peptides in the presence of water.  One such mechanism is the salt-induced peptide formation (SIPF) reaction, which can link up amino acids in aqueous solution when sodium chloride, copper(II) ions, and sufficient heat are available.  It’s quite likely that these things were available before life came about.  Other possible pathways to peptide formation in aqueous solution involve sulfur, something else that was available on the ancient Earth.

McCombs later comes up with this argument, which I haven’t heard before.  I’ll quote it in full.

Every time one component reacts with a second component forming the polymer, the chemical reaction also forms water as a byproduct of the reaction. There is a rule of chemical reactions (based on Le Chatelier’s Principle) called the Law of Mass Action that says all reactions proceed in a direction from highest to lowest concentration. This means that any reaction that produces water cannot be performed in the presence of water. This Law of Mass Action provides a total hindrance to protein, DNA/RNA, and polysaccharide formation because even if the condensation took place, the water from a supposed primordial soup would immediately hydrolyze them. Thus, if they are formed according to evolutionary theory, the water would have to be removed from the products, which is impossible in a “watery” soup.

Never mind, for the moment, that reactions that can link up amino acids in water under conditions that may have been available on the ancient Earth have been demonstrated and studied.   Let’s look at his argument.

Perhaps McCombs means to confuse us by throwing around terms like “Le Chateleir’s Principle” and “The Law of Mass Action”.  Perhaps he merely condused himself, but did McCombs really say that “any reaction that produces water cannot be performed in the presence of water“?  That’ll be news to any freshman chemistry student who has ever titrated an aqueous solution of an acid with aqueous sodium hydroxide – a reaction that produces water in an aqueous solution.

HC2H3O2(aq) + OH(aq) –> H2O(l) + C2H3O2(aq)

The titration of vinegar with aqueous sodium hydroxide is a staple of introductory chemistry labs.

Maybe that quote of his is not what he really meant to say, but nowhere does Le Chateleir’s Principle say that it’s impossible to do a chemical reaction if one of the products is already present.

After recycling more discredited creationist claims (see the links at the beginning of this post for more on those), McCombs ends his screed by saying that

The synthesis of proteins and DNA/RNA in the laboratory requires the chemist to control the reaction conditions, to thoroughly understand the reactivity and selectivity of each component, and to carefully control the order of addition of the components as the chain is building in size.  The successful formation of proteins and DNA/RNA in some imaginary primordial soup would require the same level of control as in the laboratory, but that level of control is not possible without a specific chemical controller.

The problem with this argument is that it assumes that since humans might make a specific biomolecule in the lab with the purpose of making it quickly and at a high purity, that nature has to be doing the same thing.    McCombs has provided no evidence whatsoever that this assumption is valid.  If anything, the fossil record of organisms that no longer roam the Earth says the exact opposite!


I also recommend taking a look at this article: “A model for the role of short self-assembled peptides in the very early stages of the origin of life” by Ohad Carny and Ehud Gazit. Very interesting stuff.  As always, actual science is far more interesting than creationist screeching about what can’t be done because it violates cretionist (mis)understanding of science.

The expectations gap

Wednesday, February 18th, 2009

Here’s an interesting little NYT article on the gulf between the grades students expect to receive in their college classes versus the grades they actually earn:

A recent study by researchers at the University of California, Irvine, found that a third of students surveyed said that they expected B’s just for attending lectures, and 40 percent said they deserved a B for completing the required reading.

Some college educators refer to this as the “I paid my fee, gimme my B” phenomenon.  The only thing about this study’s results that surprises me is that only a third of the surveyed students expected to get an above-average grade just for showing up.

This leads into a more revealing quote from an interviewed student:

“I think putting in a lot of effort should merit a high grade,” Mr. Greenwood [the interviewed student] said. “What else is there really than the effort that you put in?”

How about demonstrating mastery of the course competencies?  A course grade that’s higher than average should denote that a student has a higher-than-average proficiency with the material covered in the course.  That’s it.

The student continues:

“If you put in all the effort you have and get a C, what is the point?” […] “If someone goes to every class and reads every chapter in the book and does everything the teacher asks of them and more, then they should be getting an A like their effort deserves. If your maximum effort can only be average in a teacher’s mind, then something is wrong.”

Except that the grade reflects mastery of material rather than how much time a student spent sitting at his desk with his textbook and his iPhone.

It’s not quoted in the article, but from my own experiences there’s another underlying issue with student expectations.  Students think that they’re working a lot harder at a course than they really are.  I’ve had students who sincerely believe they’re putting in lots of effort towards a course when I talk to them about what went horribly wrong on their tests.  Here’s how the discussions typically run.

Student:  “I don’t understand why I did so badly on the test.  I studied really hard.”

Me: “Okay.  Well let’s see if we can work out how to get you to do better on the next test.  Let’s take a look at some of the study guide problems you worked out while you were getting ready for the test.  Maybe we can find out what was giving you trouble”   (I teach chemistry, which is very much a problem-solving course.  I give my students study guides complete with practice problems for every unit of material we cover, as well as additional practice sets with solutions on my course web site.)

Student: “Umm…”

Me:  “I think I see the problem.  How did you prepare for this test?”

The student usually says something at this point about “rereading the notes” or “looking at the book”.  While these things might be a small part of preparing for a problem-solving text, most of the actual preparation should be, well, practicing how to solve problems.

Even though glancing at the course notes and skimming over the textbook really isn’t putting real effort towards a class, most of these students I talk to about their study habits seem to think it is.  And that’s what’s really wrong with the student quote above.

With help like this …

Wednesday, February 18th, 2009

There’s an odd headline in The State today:
Bill would help SC schools amid budget cuts
Sounds good, right?  Then you read the article.

South Carolina lawmakers gave key approval Wednesday to a bill allowing school districts to increase class sizes and furlough teachers to absorb budget cuts

That’s “help”?  If cramming more and more students into a classroom and cutting teacher pay (which really isn’t that great to begin with) is meant to help our schools, I shudder to think what a bill hurting our schools would look like.

Disappearing hard drives

Friday, February 13th, 2009

So I’m checking e-mail last night, and something strange happened inside my laptop.  The hard drive disappeared.  No smoke, no odd noises.  Just … no hard drive.

As far as the laptop was concerned, the hard drive had simply been teleported from inside the laptop to inside of Bertrand Russell’s celestial teapot.  Poof!  Gone.

So today’s lessons are:

  1. Always keep backups.
  2. Always keep a spare hard drive around for your primary laptop.

An outrage!

Thursday, February 12th, 2009

Here’s a letter to the editor from a Pee Dee media outlet:

Now, I’m really sorry to say this, but the Koran really needs to be taught in our Pee Dee schools.

Our grades are starting to be lower and lower every grading period, especially in Hemingway, where three-quarters of the student body are failing.

So with Allah’s help, our students’ grades will rocket up to A’s and B’s.

Outrageous, right?  We should never allow this sort of thing to be crammed down our children’s throats in the public schools.  Our public schools are meant to educate kids, not indoctrinate them.

Okay, I admit it – I changed the text of the letter above just a little.  But how is the outrageous letter above any different from the actual letter that was published – the one that said:

Now, I’m really sorry to say this, but the Bible really needs to be taught in our Pee Dee schools.

Our grades are starting to be lower and lower every grading period, especially in Hemingway, where three-quarters of the student body are failing.

So with God’s help, our students’ grades will rocket up to A’s and B’s.

Anyone?

Stop: Rant time!

Wednesday, February 11th, 2009

It’s the day of the first chemistry test.  Since this is a low-level introductory class, we’ve spent much of the last few weeks learning how to do math for lab work rather than actual chemistry – because when students say they have problems with chemistry, they’re really saying that they have problems with math.

We’ve had extensive demonstrations of how to properly use scientific calculators for routine laboratory calculations.

Calculator

Calculator

In short, the students very well know that they’re going to be using their calculators for much of this test.

So … why do students still come to the test without their calculator?  It’s not like there’s a very long checklist of things to bring to the test:

  1. The student’s brain
  2. A pencil or two
  3. A calculator

The next thing you know, some students will be leaving their brains at home on the kitchen table.

Here endeth today’s rant.

Where did THIS come from?

Wednesday, February 4th, 2009

So, where did this come from?

Snow!  AGAIN!

Snow! AGAIN!

It’s the second snowfall here in my part of South Carolina this year.  (It’s also the second snowfall we’ve had in the last five years.)

This time, though, the college (and most local schools and businesses) didn’t issue a delay or cancellation.  That was unfortunate, since driving conditions during this snowfall were much worse than during the last one.

Let’s just say I’m thankful my car’s got traction and stability control …