A Creation Petting Zoo?

I decided to take some time and write a follow-up piece to my adventure at the petting zoo at the Creation “Museum” and fulfill Mr. Hammer’s offer of guest posting.

A little about myself… I finished my PhD in Toxicology in 2005 at the University of Kentucky and am now teaching part time at my undergraduate alma mater. I used to blog as a graduate student, mostly on politics and religion, and gradually slacked off. After the SSA visit to the Creation “Museum”, I decided it was time to come back, and put together a blog on what is happening in the biological sciences today, and how you could present that information in a manner that would engage students and promote learning. Daniel offered to let me write up a guest post on the visit, and so, here I am.

You can probably guess how I responded to the faux science of this place. The good news is that it seems like an incredibly boring place to take a kid. The bad news is that lots of kids get hurried through there, and find themselves lied to about how science works. Of course, that makes my job harder, because the theory of evolution is a central concept in biology, and without it, there are lots of unconnected lines of evidence, begging for something to unite them. Answers in Genesis hopes to provide a replacement concept in a very narrow interpretation of Genesis, and hell take you if you dare to disagree. The problem is, even if they were able to disprove evolution by natural selection, it wouldn’t make a six day version of biblical creationism, by default, correct. The worst part is that they can’t even come up with any new claims. They are stuck with arguments that are decades, sometimes more than a century old, and all long debunked. Even intelligent design isn’t a new concept.

Science is a system by which we attempt to remove our bias and prejudice, and seek naturalistic and materialistic explanations for what we find in the world around us. The supernatural doesn’t enter into our examinations, unless somebody makes the claim that the supernatural can be measured or otherwise proved to exist. So far, nobody who makes those claims has been able to offer any concrete evidence for their claims and while it is impossible to disprove them, the “Museum” is being academically dishonest and is ethically bankrupt by plainly admitting that they start with a conclusion and ignore any evidence that doesn’t support their conclusion. They abandon any pretense of science from their starting point and they don’t even know it.

Keeping up with the amusement church theme found on the rest of the grounds, Profit Prophet Ham has a lovely little petting zoo, perhaps one of the two interactive exhibits available to catch the attention of children.

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Tuesday Toxics – Copperhead!

A couple weeks ago, our department had its yearly retreat, which we always have at one of Kentucky’s state parks. This time it was at Jenny Wiley State Park, which was nice, and the cabins were excellent. On the way home I stopped off at Natural Bridge State Park, thinking I would hike up to the top, which I remembered was a pretty easy walk. Yeah. I was probably about 10 then, and in much better shape and full of the boundless energy. I didn’t bring a water bottle, it was hot, and I parked about as far from the top as I possibly could.

Sheesh, I am out of shape. I wisely gave up before the steepest part and went back to look for something a family that I passed on the way up mentioned. A copperhead snake (Agkistrodon contortrix) was just a few feet off the trail, and I had to get a picture. Crikey! I wandered back down the trail and heard a couple talking about the snake. The woman decided to walk down the trail, while the husband tried to provoke a reaction from the snake by poking it with a stick. Are some people intentionally stupid? Of course, he couldn’t get one of the most stand-your-ground venomous snakes to nudge, so after about 30 seconds he wandered off.

If he had tried to reach down to try to grab the snake, I would have shouted at him to stop, but up to this point he wasn’t anywhere near getting bit. Take this as a hint, don’t harass snakes. Even non poisonous ones can give you a bite that easily becomes infected. But don’t be horribly frightened of them, either. Just back off if they offer a threat display and if you don’t know what you are doing, don’t try to pick them up. Most poisonous snakes rarely bite unless you try to pick them up or attack them. People have even stepped on and near cottonmouths and other pit vipers (family viperidae, subfamily crotalinae) with no response, and they will run (slither) away in preference to striking. One of the fascinating things about the pit vipers is that they can give a dry bite or only inject enough venom to let you know they mean business. They don’t want to waste their venom.

Copperhead camouflage is so effective that they will just sit still rather than flee (not that they know it, its is probably an evolved instinctive behavior), so the first threat display from the well hidden copperhead is to give a dry bite, making them unusual for pit vipers. These little guys would really rather just be left alone. If you are working in an area known to have copperheads, be careful when cutting fallen logs or clearing brush. Many experienced woodsmen rev their chainsaws for several minutes before they start cutting a fallen tree to give any copperheads a chance to slither away.

But hey, enough safety with critters, pictures!

Copperhead

Copperhead

Without the flash, this little guy just about disappears. I completely missed him the first time I walked past. Their hourglass scale pattern is perfect camouflage against a background of dry leaves.

Copperhead camoflage

Copperhead camoflage

This species is named for its copper colored head.

Copper head

Copper head

I have to say, this is one of my better nature photographs. I’ll probably have the original printed and put it up in my office. The detail is incredible, as seen from the image of the head, which is full size, and the scales, which are half size. I am considering putting a few of my nature photos up for purchase. Let me know what you think.

OK, now a bit of the biology of these guys.
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The Creation “Museum”

Why would I go to a creation museum?
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I don’t believe in a special creation, to put it bluntly. I have no question that evolution by natural selection is fact as well as solidly grounded theory.  I find the whole concept of a 27 million dollar facility pushing a narrow interpretation of a creation myth to be offensive, when one could have sent those millions to, say, upgrade the facilities of a teaching hospital in Africa, or fund clinics in the slums of central America, or promote polio vaccination programs worldwide… the list of real charitable projects would go on and on and on. And if you would prefer those dollars be used for US charities, try Habitat for Humanity or the Susan G. Komen breast cancer charity, or the Secular Students Alliance (more on this group in a post to come).

Why? Because my students come from varied backgrounds and with this “museum” only a 90 minute drive from home, some will have visited this place. While I am familiar with most of the claims of creationists of many stripes, thanks to TalkOrigins and The Counter Creationist Handbook (which I am holding above, and if you are a science educator, you should own this book and keep it in your office or classroom), it is always best to see these claims firsthand so that you can see their claims firsthand, how they are presented, etc so that you can be better prepared to respond.

Also, because there was a large group going, I didn’t have to pay $22 to get in, just ten. I’ll be offsetting that with donations and dues payments to a variety of pro science education groups or skeptical organizations, such as the NCSE, CSI and SSA, among others. Consider it Idiocy Offset Credits, sort of like offset credits of the carbon type.

Finally, PZ Myers, lord of the squid, was going, and I wanted to get a chance to see if fire really did shoot from his eyes and if bats darkened the skies with their leathery wings above him, blotting out the sun. Sadly, his reputation in this manner has been greatly exaggerated.

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My tie has the periodic table on it. I was ready to teach the controversy between four elements and all those hundred or so elements that scientists keep adding to every now and then. PZ’s tie, on the other hand is one of two crocoducks, the other belonging to Richard Dawkins.

What did I find? Continue reading

Nucleic Acids

On the politics website, AmericaBlog, there was a discussion about the resurgence in interest in the H1N1 swine flu. A question there inspired this post.

What are the differences between RNA and DNA?

Both RNA and DNA are nucleic acids, which store genetic information. DNA is long lived, stable, and is what everything but some viruses use for information storage. The D stands for deoxyribose, a sugar that is part of the backbone of the nucleic acid making DNA deoxyribonucleic acid. The R stands for ribose (ribonucleic acid), another sugar, very similar is structure, but differing slightly enough that it isn’t as stable. The difference between the two sugars is just the presence of an oxygen on ribose, where you would find a hydrogen on deoxyribose.

DNA and RNA with their different structure highlighted

DNA and RNA with their different structure highlighted

Everything but RNA viruses use RNA primarily to carry information from DNA storage to structures called ribosomes, which read the information and make proteins according to it. RNA viruses use RNA for storage and to code directly for proteins.
So what is a retrovirus?

It is virus that uses RNA to store its genetic material, but it does something different. Everything but retroviruses follows a pattern called the “Central Dogma.” DNA is transcribed (copied) to RNA. RNA is translated (decoded) to protein. Just about everything except for those RNA viruses replicates its genetic information at step A, including us. RNA viruses, to my knowledge are the only ones that replicate using step B. Never does this go backwards, or at least thats what we thought.

The Central Dogma of Biology

The Central Dogma of Biology - modified from http://faculty.uca.edu/johnc/central%20dogma.gif

Retroviruses run this system backwards, so we call them retro, as in backwards. They carry an enzyme that can reverse the process of transcription, called reverse transcriptase, taking RNA and making DNA copy, at step C. This DNA copy is then inserted somewhere into the host’s DNA where it can begin producing RNA copies of itself.  Some will be used to code for proteins and enzymes that make up the virus, while others will become new viral genomes. As part of this cell’s genome, when it divides, you now have two infected cells. Then four, eight, sixteen and so on.

Because it is in infected cells as part of their chromosomes, they are there forever. We can’t get rid of them. HIV, a retrovirus, infection is forever, but treatable, unless a new conceptual procedure can be repeated in more patients.

Endogenous retroviruses

Since retroviruses become a permanent part of a cell and its descendants, if that cell is a germ line cell, meaning sperm or egg producing cells, the virus can be passed directly on to the offspring (HIV doesn’t infect germ line cells, so this isn’t one of the routes that children can become exposed to HIV). We call these endogenous retroviruses.  If the virus isn’t something that kills the infected individual before they can reproduce, it can become part of a larger population. Over time, those viruses can become mutated to the point that they can’t produce new functional viruses. At that point, the virus is dead, and may become further mutated. If you look in the human genome, you will find six or seven of these dead viruses, silenced over hundreds of thousands of years of evolution.

Teach on.

Teaching about swine flu

These are some notes I put up on the JREF forum last April. I have updated a bit of it, fixing some minor errors. I figured this would be a good place to start things off.

I moved a bit away from my planned lectures on environmental science for my two freshmen biology sections to focus on this current and very teachable event, and thought that other educators may find these lecture notes and resources useful.

First off, the google swine flu map provides an excellent resource for teaching how modern transportation can make preventing the spread of flu practically impossible. Unlike the original google map, this map has a very easily understood legend. For details on national and regional outbreaks, zoom in. For instance, Kentucky, my home state, currently has an orange circle with 167 in it. This means that there have been 167 confirmed cases, but no deaths. Florida on the other hand, has a tri colored circle with 2895. Click the circle, and you get these details.

Suspected Cases: 1
Confirmed Cases: 2865
Fatal Cases: 29

For more detail, zoom in further. Miami-Dade has these details, plus information on some cases.

Reported Location: Miami Dade County, FL
Confirmed Cases: 917
Fatal Cases: 10
This is an aggregated report based on 24 reports near the same location.

Next up is the structure of the virus. All viruses have genetic material that is either DNA or RNA, proteins that surround and protect the genetic material, and spike proteins that allow it to interact with the environment and bind to target receptors on the cells it can affect.

The flu virus has RNA for genetic material, and typically has 8 short stretches of RNA, which exist in a fashion similar to mini chromosomes. It also has two spike proteins which also are the antigens that our immune system recognizes, and give the name and classifications for these viruses. Hemagglutinin targets the virus to infect a specific cell type, and is the H of the H1N1 of the current flu type. Neuraminidase helps the virus bud off of the cell, and is the remaining N. For each different group of flu virus, HxNy describes a related group with lots of strains with minor mutations between them.

Since most of us have had H1N1 flus or flu shots recently, we have some minor immunity to members of this group, which is great news. However, mutant strains may be different enough to sneak past our immune system and make us sick. Because the flu virus mutates quickly, this is why you need to get a flu shot every year. The strain is a little different every time. In the case of the H1N1 swine flu virus, it isn’t a minor mutant, but a new combination of genes, so we really don’t know if previous shots will offer any help at all.

Also of interest is that the flu virus is an envelope virus. As it buds off of the host cell, it surrounds itself with some of the host’s cell membrane. This means that the host cell doesn’t die when viruses are released. It may die later if the virus causes the cell to use too much of its own resources to make viruses, or if the immune system detects the infected cell and targets it for killing.

I mentioned that the genome is set up as mini chromosomes, each with one or two genes, and this is very important to this particular strain. You may have heard that his flu virus has a mix of avian (bird), swine and human flu genes. Well, this is unusual, but not unheard of, and is certainly not evidence of genetic engineering and conspiracy as some CTrs (conspiracy theorists)  are claiming.

Recombination of flu genes

First, many different groups of animals have their own flu viruses, but only these three groups do a particularly good job of infecting humans. Lets say we have a hog farm, maybe with some ducks and pigeons in the area, and of course, humans.

The birds pass one virus to a hog, which is also infected with its own flu virus. This means that the animal (Animal I in my blackboard notes) has two different viruses in it’s cells. The mini chromosomes would sort separately, just like chromosomes in meiosis, and each new virus would have a random mix of bird and swine flu genes.

Lets say this gets passed along for a bit from one pig to another, or perhaps back to some birds. At some time, another animal (Animal II) becomes infected with the hybrid virus and a third virus, this time from a human flu group. Again, we have a mixture of genes being produced, and the most fit ones (not necessarily the ones that cause the worst disease) spread through the population.

If the genes are just right, the virus ends up moving into the human population and can be spread from one person to another.

Also of great value is the HHMI’s biointeractive website. Under the lecture tab, holiday lectures, infectious disease, you can find the 1999 lecture, which is a little out of date, but there is one part of the 4th lecture that specifically deals with the flu, and you get most of the above information.

The Holiday lectures are targeted towards advanced high school students, but I think that the lecturer probably used words and terms that were a bit more advanced than are needed. I don’t mind showing it to my college students, but even so, I know that some probably still didn’t follow parts of it. Alas, you can’t reach them all.

One question I received on the JREF: What are the chances for a mutation to make it particularly deadly? That’s my biggest concern?

Well, it is possible. Since the flu is an RNA virus, the rate of mutation (1/10,000) is about the same as the length as the entire viral genome, you could expect every virus to have a mutation. Most of these do nothing (no appreciable change to the 3D shape of a protein), and some will be negative and inhibit the mutant and its offspring. Occasionally, a strain will get really a really nasty mutant coming from it, but that is completely unpredictable.

If a disease kills quickly, though, it won’t get a chance to spread very far, and the outbreak would burn itself out. That isn’t very likely for the flu though, because even really bad cases take several days to progress to pneumonia or cytokine storm (extreme immune response, very nasty), including time where you are feeling OK enough to be around people. The 1918 pandemic was around 2.5 – 5% mortality, and so far, this one isn’t nearly there (even though we don’t have good numbers yet).

It is hard to estimate the case fatality ratio, because we tend to undercount the number of real cases, especially if people don’t need to go to the hospital for mild cases. The we have to figure out how many people actually died from flu and not something else, so that number is hard to get. Divide deaths by cases, and you at least have an idea of how bad it is.

Of course, we now have some anti-flu drugs and better medical care, so at least the developed world shouldn’t be affected as badly. The reason we are so concerned about bird flu is that some strains of it don’t appear to respond to these drugs, so we may have one less tool to use (at least from the few cases that have been seen).

Best, and teach on.