Posts Tagged ‘chemistry’

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.

Fingernail growth

Friday, December 12th, 2008

A little while ago, about 384 hours if you want to be exact, I was in the lab doing an experiment with some of my students.  The experiment involved isolating proteins from milk, then doing some chemical tests to show that what the students had isolated was actually protein.

One of the tests the students used on their isolated protein was the xanthoproteic test.  This is a simple test for proteins that works on proteins containing an aromatic ring, and involves the addition of a nitro group to the ring by reaction with nitric acid.  If a protein or amino acid with an aromatic ring is present, the test will give a yellow color.

You may, if you’ve ever been in an introductory chemistry lab, heard your teacher warn you about nitric acid.  In addition to causing you some pain, it will also turn your skin or fingernails yellow.  This is the same sort of chemistry in the xanthoproteic test.  Your skin and nails, after all, contain proteins.

Now, back to 384 hours ago.  While I was cleaning up the lab after my students had left, I spilled a small amount of nitric acid onto the top of my finger.  Sure enough, my finger turned yellow, along with a small part of the fingernail.

Here's the nitric acid stain.  I originally spilled the acid at the point where my skin meets the fingernail.  It's moved a bit, now.

Here's the nitric acid stain. I originally spilled the acid at the point where my skin meets the fingernail. It's moved a bit, now.

384 hours after the spill, all the yellow skin had been replaced.  But the nail has to grow out.  We can find out how fast my fingernails are growing with a simple measurement.

Here's a (somewhat crude) neasurment using a ruler from the lab.  The nitric acid stain has moved about 0.18 cm.

Here's a (somewhat crude) neasurment using a ruler from the lab. The nitric acid stain has moved about 0.18 cm.

So, my fingernail has been growing at a rate of (0.18 cm) / (384 hr) = 0.00047 cm per hour.  That works out to be 3.4 mm per month, which is right about what Wikipedia claims for the average rate of fingernail growth.

Now who says you never learned anything useful from chemistry?

Friends, does your milk powder taste different lately?

Monday, September 22nd, 2008

It looks like there’s trouble in China.  Supplies of milk powder meant for Chinese infants are tainted with melamine – the same chemical found in last year’s dog-food scare.

On Sept. 17, China’s minister of health, Chen Zhu, announced that three babies had died, more than 150 were suffering from acute kidney failure, and an additional 6,000 infants had become sick after drinking milk made from milk powder tainted with melamine.

Now you might be wondering why on earth a company would add melamine to powdered milk.  Could it have been accidental?  Or was there some reason to add this compound?

Consider this:  The amount of protein in foods is often determined based on total nitrogen content.  That’s because proteins contain a fairly regular amount of nitrogen – about 16% by mass.  Take the total nitrogen content, multiply by a conversion factor, and you have a good estimate of protein content of the food.

Take a look at melamine.

Melamine, C<sub>3</sub>H<sub>6</sub>N<sub>6</sub>.  Nitrogen atoms are indicated in blue.

Melamine, C3H6N6. Nitrogen atoms are indicated in blue.

Simple assay methods for total nitrogen content can’t distinguish the nitrogen in melamine – which is about 67% nitrogen by mass – from the nitrogen in proteins.

The tested substance appears to have a higher protein content than it actually does – since analysts assume that almost all the measured nitrogen comes from actual protein.  This is a reasonable assumption for uncontaminated materials, but is open to abuse by the amoral.

It amazes me that the Chinese were caught by this same ruse again.  You’d think that after finding melamine added to pet food, the Chinese government would have gone ahead and made sure nobody was adding it to food for humans.

The aluminum bromide reaction

Wednesday, August 13th, 2008

[This is an update of an earlier post on this blog.  This version includes streaming video]

Let’s say you don’t want to do the thermite reaction, but you still want to see some flashy chemistry. The reaction between aluminum and bromine might fit the bill.

2Al(s) + 3Br2(l) –> 2AlBr3(s)

It’s a very simple-looking reaction – a little electron transfer from aluminum to bromine.  Like lots of these reactions, it’s exothermic.  Exothermic enough to put on an impressive show.

Enough heat is generated by the reaction to vaporize some of the unreacted bromine – throwing off orange smoke.  On top of that, the aluminum gets hot enough to melt and spark.  For obvious reasons, this reaction should only be done where you’ve got very good ventilation. I used my hood for these pictures and this video.

Here’s a still image of the reaction vessel containing only liquid bromine and its vapor.

Liquid bromine and its vapor

Liquid bromine and its vapor

Bromine is the dark red liquid at the bottom. Bromine is quite volatile, and you can see orange bromine vapor in the top of the beaker.

About ten seconds after adding some torn aluminum foil, things look more like this.

Aluminum bromide reaction, 10 seconds after adding aluminum

Aluminum bromide reaction, 10 seconds after adding aluminum

A little later …

After a few more seconds, it's hot enough to spark

After a few more seconds, it's hot enough to spark

And then …

Oh yeah!

Oh yeah!

… but you didn’t read all this way for still pictures, did you?  How about a video?

After the reaction’s over, you’ll want to buy a new beaker.  The melted aluminum foil fuses with the bottom of the beaker.  (The sand bath is there to catch anything that gets through the bottom of the beaker when it breaks!)

Aluminum melted into the glass at the bottom of the beaker

Aluminum melted into the glass at the bottom of the beaker

So where’s the aluminum bromide?  Some of it has stuck to the sides of the beaker.

Aluminum bromide (white / yellowish solid) on the beaker

Aluminum bromide (white / yellowish solid) on the beaker

Aluminum bromide formed will react with water, causing the release of acidic hydrogen bromide vapors, so you need to be careful disposing of the product! That reaction is also very exothermic, so touching the product or adding water to it is not recommended. Leave it out long enough, though, and it will absorb water from the air on its own.

Ain’t chemistry neat?

Disclaimer: Do not try this reaction at home. In fact, do not try this reaction at all! You were warned.