Science Ruminations

squirrel aquarium

This is a funny clip Tim filmed after we found a squirrel gnawed off a large plastic portion of our bird feeder at Tranquility Base (our undisclosed location in the middle of Lake Michigan).

If you have your audio on you can hear Tim muttering to himself.

We now feed the ravenous creatures ears of corn and are wondering how we might regret it later. But they are so damn cute! I am happy to be feeding them. The birds now have their very own squirrel proof feeder thanks to droll yankees products.

bird flu dog treats update

Would you believe my post complaining about chinese dog treats was posted Feb 2006? This over a year before the pet food recall scare.

I have long been trying not to buy Chinese products (it isn't easy!) and it seems my fears were well-founded.

Bird Flu Flavored Dog Treats?

As an obsessive label reader, it should not surprise anyone that I compulsively read the label of a bag of dog treats selling in a Costco store, out of sheer curiosity (I have no dogs.)

The treats are made of 100% chicken. But what bothered me was that this product was "a product of China".

What do we know about Chinese chickens that is worrisome these days?

What do we know about the Chinese chickens that are most likely used in pet food, the sick ones most likely to be discarded because they are not considered fit for human consumption?

Will some kind virologist reassure me about this? Perhaps the survival of bird flu viruses is compromised in those bags...bags that are neatly sealed to keep in the moisture...But I am not a specialist in this area so I don't want to spread any panic or alarm. I could be all out at sea. But I keep thinking about it...

Inappopriatedly named Quark

I am contemplating my Maine Coon cat Quark. This is one of the largest breeds of cats, and he weighs in at about 18 pounds. Since a quark is a tiny particle, this is a paradox. We do joke that he is "has a hull made out of solid neutronium!" (If you know which Sci Fi series that is from you are even more of a geek than I am.) So, he could be made out of Quark material, which could explain his density.

I just wish I had named him Jupiter instead. Because he is massive and has a spot.

Absolute zero

Absolute zero is the coldest temperature possible. Atomic motion would cease. School would be cancelled.

PDRhealth website error persists

I just noticed a glaring error remains on the PDRhealth website page for flaxseed. I emailed them as best I could about this over a year ago, and got the typical automated email reply that everyone knows actually means they just electronically dismissed you, and short of yelling on a megaphone outside some poor bastard webdesigner's house and risking arrest, no one will spare their attention for your comment.

The image for alpha-linolenic acid is not alpha-linolenic acid. It is something else entirely (it looks like some phosholipid derivative).

Now, I know very well that errors like this happen to the best of us. How do I know this? My students point out when I err in my lectures with annoying frequency, bless them. I encourage to them to aggresively point out when this happens, and then I announce, "Let me publically humiliate myself by pointing out my error lest you do the same!" They seem to enjoy this, and it does help in the goal of teaching.  I just try to swallow the irritation I feel for making the mistake in the first place

But we should all just try extremely hard not to make mistakes, and remain  vigilant about looking for them and correcting them. Otherwise, as I like to tell my students, our patients will die.

So, let's see how long this error persists on this page. Not that most people care what molecules look like. But I care very deeply what they look like. And a fatty acid should not look like a phospholipid. That is just embarrassing.

Of Almonds and Cinnamon

It struck me as I lay awake last night, I had never realized how similar benzaldehyde (the principal flavor note from almond oil) is to cinnamaldehyde (the principal flavor note from cinnamon oil):

  Both have an aldehyde in conjugation with a benzene ring.

Then I wondered about how different they were, of course, cinnamaldehyde is much more irritating. Many aldehydes are irritating to the skin. I wondered what molecule you would get by increasing the length of carbons between the aldehyde and the benzene ring, and maintaining the conjugation.

Would it make if more cinnamony and less almondy? Or be something else altogether? Are  taste buds, as receptors, are more digital than analog, and bind something or not, so you get one impression, or not?

But then again, many receptors experience partial binding to ligands, so maybe you can have partial binding of a similar looking molecule and get a similar impression, but slightly different. This seems to be the case with various small carbohydrates like glucose and maltose and sucrose, which all have similar structures, yet subtly different flavors.

Then again, you have have very similar looking molecules like these, and drastically different tastes.

Finally, I would really like to know the natural origin, if any, of some molecules that have a longer chain between benzene and aldehyde, maintinaing the conjugation between the two. I want to know how its charactistics compare with these two.

New Year's Resolution

In 2006 I resolve to not create little book displays of my brand new, recently published book when I go into bookstores, by turning the cover of my book outwards for all to see. I also resolve to refrain from turning other authors books onto their backs. Except for anything by Kevin Trudeau. He is an idiot boy.

Non-comedogenic

Do you know what non-comedogenic facial products are? They are facial products that are not funny.

Corky molecules

I just celebrated my 40th birthday with black balloons and a surprise party (it wasn't entirely a surprise because Tim engaged in suspicious atyical house cleaning activities beforehand, but nontheless the unexpected shouting  of "surprise!" procured a loud profanity from my mouth  which seemed to please everyone.)

One of my former students, Fred, a former brilliant chef turned doctor of pharmacy student (I am so proud that he is studying capscaicin! And I showed him his first benzene ring! Parental pride...) showed up with a bottle of Chateauneuf-du-pape, which I was really looking forward to trying, because I had read good things about it. Sadly, Fred pronounced the bottle corked, so I never got to learn what it was like.

I lay awake at night wondering what could be the corky molecules? It smells and tastes like wet god, I mean wet dog (yes I am dyslexic but that is so funny I could not erase it), not that I have ever tasted a wet dog. What makes a wine taste corked? A month later, I decided to look this up. It is apparently TCA, or trichloroanisole:

Looks a bit PCB-ish, doesn't it? It is apparently the result of an airborne fungus (OK, which one?) metabolizing chlorine contaminants (pollutants and herbicides) from cork trees. There you go.

Imino sugars

I have just discovered imino sugars. I can't believe I have not run across them before. I still have to learn more about them, but this is what I know so far. These molecules look very much like sugar rings. That is, they are covered with hydroxyl groups and are ring shaped. Yet, where you would expect to see the ring oxygen, there is a nitrogen in its place.

These are common in plants, one article says in tomatoes and potatoes (partlicularly nightshade plants or just plants in general, I wonder?) and "crips" (OK this is the cute British term for potato chips, which are not preciselya plant. I think it is amusing that the British author lists "potatoes, tomoatoes and crips" as if they were all different plant sources of imino sugars.)

I first was clued into the topic of imino sugars by a podcast from biotech nation. It was watered down as far as technical detail, so I had to look up more info. I was a bit annoyed by the podcast, as it went on about how wonderful it is that some of these imino sugars nonspecifically provoke the immune system. This could (they hope) be helpful in fighting tumors in cancer patients. I certainly hope they are right, but of course, inflammation (ie, an overly provoked immune system) can make metastasis more likely, and can exacerbate cancer, so it bothered me a bit. Wouldn't you want to target the immune response and make it more specific? But I do not know, I should read more.

One imino sugar has been N-alkylated to create something called meglitol, which is used in diabetes treatment. I thought at first that, based on the name, it would be like the meglitinides, which stimulate insulin secretion. But no, meglitol has a quite different structure from the meglitinides. Meglitol is an alpha-glucosidase inhibitor, that is, it prevents the digestion of starch and certain other saccharides, so I suppose you do not absorb the simple sugars. So it lowers blood sugar after eating.

A lot of these imino sugars apparently resemble the transition states of alpha-glucosidase doing its thing, so they mess with sugar metabolism in various ways. When I described this action to Tim he said with his usual flair for delicacy, "So it could be an anti-fat ass medication?" I have not heard it described as such, but again, if people can make that logical leap, we have to watch out for the usual parade of hype associated with a new natural diet aid crapola.

Now, what dose of imino sugars are we getting when we eat the plants that contain them? And what is their potency at these doses? Insignificant? Or what?

I understand many occur as glycosides, so you perhaps need active gut bateria to cut off their attached sugars to make them active?

Finally, what do they taste like? Are they bitter because of the basic nitrogen? Looking at meglitol, there is no adjacent place for nitrogen's basic electron pair to be withdrawn onto via resonance. So it looks basic to me.