Theoretical physicist Dr. Lawrence Krauss gave a talk at AAI 2009 titled "A Universe From Nothing." Lawrence summarizes much of what we know about the universe and how we know it. The lecture was engaging, entertaining, and accessible for the lay audience. If you're at all interested in where we came from and how it will end, you'll enjoy this talk.
Monday, November 16, 2009
Monday, October 26, 2009
Get Vaccinated!
I'm planning on getting both of the flu vaccines this year - seasonal and swine. Because you know, I hate being sick, and getting inoculated will lower my chances of getting sick. It will also lower my chances of getting other people sick, which is why it's so important for people to (a) get vaccinated even if they are in low risk groups, and (b) STAY HOME IF YOU GET SICK! I don't mean you can't go to the store to buy food, but please, for the love of dogs, don't go to work or to class and give your viruses to everyone you know. Keep them to yourselves.
Whenever I think of the war between viruses and humans, I get to thinking about evolution. Evolution is a fact of the universe, and viruses are an excellent example of how it works.
First, a little virus 101. A virus is a packet of DNA (or RNA) held together in a multi-purpose protein coat that both protects the genetic material and injects it into a host cell. Viruses are not considered living things because they cannot reproduce themselves. They need the machinery of the host cell to replicate both their genetic material and their protein coats.
Even though viruses are not technically living things, they still undergo evolution. Virus use the same kinds of genetic material that we do. (In fact, viruses work because they use the same genetic code that all living things use. If they used a different code, they wouldn't be able to use host cells to replicate.) DNA replication is not perfect. The process produces an error every million or so nucleotides. That isn't a whole lot, but when you're pumping out billions of viruses, you're guaranteed to have some with DNA errors. It's just a fact of how the biochemical processes of DNA replication work. Furthermore, after DNA has been replicated, the copies can be damaged by chemicals and radiation (viruses don't wear sunscreen) which can lead to mutations. So, out of the billions of viruses pumped out by a single infected person, some of them are going to be mutants. Most mutants will be less proliferate than their non-mutant siblings, but some will be as good as or better than their siblings at surviving and proliferating. Since viruses are under constant attack by our immune systems, the ones that are most effective against our immune systems will naturally come to dominate the virus population.
It isn't necessarily about traits that make the virus intrinsically better at survival inside a generic host. If a virus achieves a neutral change to the shape of its protein coat, that can help it to escape recognition by a host that has had that viruses ancestor in the past. You can get basically the same type of flu every year, so long as it has mutated enough that your immune system no-longer recognizes it. And there's nothing you can do to stop viruses from evolving. As long as there are hosts for the viruses to infect, and as long as there are mutagens and imperfect DNA replication, there will continue to be new variations of viruses, and the most prolific variants will spread. Random change + nonrandom reproductive success = evolution.
Tuesday, October 6, 2009
Unintelligent Design (Part II)
I promised I'd tell you about the unintelligence of RNA transcription, so here it is. To understand just how stupid our cells are about this, we must again contrast our process with that of bacteria.
Most organisms store the bulk of their genome in DNA. The double helix is more stable than the single helix of RNA. DNA is a long list of genes, you can think of them as recipes in a cookbook. (It isn't set up like a logical cookbook. There are long spans of gobbledygook between the genes. Eukaryotes like mammals, bugs and trees also have spans of gobbledygook within their genes, which have to be edited out each time the gene is used.) DNA is the master copy of the cookbook. It's stored in the nucleus, away from all the ingredients, so the pages don't get torn, singed or spilled upon. In order to make the recipe, you have to copy it first. That's fine with the cells, because the machinery that uses the recipes can only take RNA anyway. That's the job of an enzyme called polymerase. In eukaryotes, the polymerase transcribes the gene into RNA in the nucleus, and the RNA is taken out of the nucleus to be put to further use. Bacteria have don't have nuclei, but they still have to make the RNA copy of the gene in order for their machinery to put it to use.
Both bacteria and eukaryotes have promoters - sequences at the begining of the genes that basically say, "start here." Bacteria and eukaryotes also have sequences that signal the end of the gene, but they work differently. In bacteria the "end" signal is called a terminator. When the polymerase reads the terminator, it detaches from the DNA and releases the RNA copy to be used by the cell. Makes sense.
When eukaryote polymerase gets to the "end" signal, it transcribes it and keeps on going. The transcribed end signal causes proteins that have been monitoring RNA transcript to cut off the transcript and take it away for processing so it can be used by the cell. Meanwhile, polymerase keeps going like a runaway train, transcribing hundreds of nucleotides, whatever happens to follow the gene. Biologists haven't completely figured out what happens next, but here's what it looks like: An enzyme comes up and digests the trail of RNA gobbledygook that the polymerase is spewing out, recycling it back into unattached nucleotides. When that enzyme reaches polymerase, it knocks polymerase off the DNA, and transcription stops.
To summarize, bacteria have a system that works perfectly. We organisms with nuclei have defective polymerases that no longer recognize the ends signals. Rather than fix the polymerases, evolution threw us some proteins to salvage the RNA transcript and then another enzyme to clean up the mess and slide tackle the runaway enzyme off the DNA. That deserves a very special contraction: untelligent. Keep in mind that every time polymerase attaches a nucleotide to the RNA strand, it's using energy - the equivalent to one ATP molecule. We don't get that energy back when we recycle the nucleotides. What kind of Intelligent Designer would have left such a mess?
Then again maybe there is some wisdom here. Bacteria are better at both DNA replication and RNA transcription. Maybe the Designer made the universe for the bacteria, and we're just here to be their hosts. After all, for every human cell in your body, you also have ten to twenty bacteria living in and on you - in a magnificent diversity of 500 - 1,000 different species. That's about 1012, or 1 million × 1 million, bacteria living in and on each and every one of us. All hail our glorious Bacterial Creator?
Wednesday, September 30, 2009
I thought I had a "God-shaped hole" in my life...
...but then I got a dildo.
Happy Blasphemy Day, everyone! The Center for Inquiry has designated September 30th International Blasphemy Day.
Blasphemy Day takes place September 30th to commemorate the publishing of the Jyllands-Posten Muhammad cartoons. The purpose of Blasphemy Day is not to promote hate or violence; it is to support free speech, support the right to criticize and satirize religion, and to oppose any resolutions or laws, binding or otherwise, that discourage or inhibit free speech of any kind.Read more here.
Wednesday, September 23, 2009
Unintelligent Design
I'm taking some biology classes, thinking about applying to some grad programs. I'm learning a lot - mostly cellular biology right now. But the more I learn, the more obvious it becomes that life was not intelligently designed. It's really hard to believe anyone who has more than a tenuous grasp on basic biology can believe in ID, especially that the IDer was the all powerful, all omniscient God. Vestigial organs, vestigial genes, and tons of other obvious design flaws litter the biological landscape. I'll talk about RNA transcription next time. First, I'll tell you about the crazy hack embedded in our DNA replication.
(I've gotten kind of technical, and I've tried to keep it short, so please do email me if you don't understand something, and I'll try to update the post to make it more readable.)
Updates posted on Oct 6 follow the original post.
Telomeres are what is known in the software design world as a "hack" - a quick and dirty fix to a bug or design flaw. To understand telomeres, you have to know a little about DNA and DNA replication. (I've attempted a terse explanation here, but there's always Wikipedia for a more thorough description.) A single strand of the DNA double helix consists of a string of nucleotides. These nucleotides contain the familiar A, C, G and T bases that are held by 5-carbon sugar rings, and the rings are connected by phosphate groups. These sugars are not symmetrical. They have an oxygen atom in one part of the ring, and a carbon atom sticking off the side. Biologists have labeled the carbons 1 - 5. The 3' carbon and the 5' carbon are the two that bond to the phosphate group, and to make a strand of DNA, you have to keep all the nucleotide lined up the same way: 3' - 5' - phosphate - 3' - 5' - phosphate and so on.
The problem is, the enzymes that assemble new DNA strands can only add nucleotides to the 3' end, not the 5' end. I'm not going to go into it here, but that causes an ugly little work-around called Okazaki fragments during the normal part of DNA replication. Where the real problem happens is at the ends of the DNA strand. You end up with a little bit that's too close to the end of the template to code on. If you could add to the 5' end, it wouldn't be a problem because you could work backwards from that end, but since you can only add to the 3' end, and you don't have the room to work there, you end up losing a little bit of your DNA every time it replicates.
The hideous hack we use to get around this is, whenever you make a gamete (sperm or egg) a special enzyme adds telomeres - non-coding nonsense DNA - to the ends of all of your chromosomes, so that as they fall off, it won't eat into your genes... until your cells have replicated for a bunch of years. When humans were only living into their 40s, this wasn't so much of a problem. Now, this might be one of the causes of aging. Your cells are losing their instruction manuals page by page, each time they divide.
There are two obvious fixes that an intelligent designer could have used. As previously mentioned, she could have engineered an enzyme that could add to the 5' end of the DNA. This would solve two problems and make your DNA replication much more efficient, both in time and energy consumption. The second fix is already used by bacteria. She could have stored the DNA in long rings, or just connected the ends during the final steps of replication. Bacteria store parts of their DNA in little rings, and those rings don't have the problem because they can build the last part of their DNA off the place where they started. I don't know how making a ring out of our DNA would affect chromosome storage, but you wouldn't have to keep it in a ring all the time. We have enzymes in our cells that cut DNA apart and paste it back together, so the rings could just be connected during the last parts of DNA replication. An intelligent designer would have been able to see these options and make the choice. Evolution blindly fumbled around for whatever worked, and we ended up with telomeres.
Update: Check out this short video of DNA replication:
Update:
On Oct 5, Nobel Prize for Physiology or Medicine was given to three scientists for their work finding telomeres and telomerase - the enzyme that creats them. From the press release
Elizabeth Blackburn and Jack Szostak discovered that a unique DNA sequence in the telomeres protects the chromosomes from degradation. Carol Greider and Elizabeth Blackburn identified telomerase, the enzyme that makes telomere DNA. These discoveries explained how the ends of the chromosomes are protected by the telomeres and that they are built by telomerase.And to complete this amazing coincidence of my writing this post and telomeres turning up in the international press, at least one prominent ID promoter has claimed telomeres as support for ID. In an article DLH posted on Uncommon Descent:
These telomeres can probably be shown to be essential to survival, and are likely to be irreducibly complex. If so, how can macro evolution explain the origin of this marvelous preservation feature that appears to be an Intelligent Design?Gonna do some research to show that they're irreducibly complex? Nope. Gonna do a little googling and find out that there are other, arguably better ways to solve the problem that telomeres fix? Nope. IDiot..
Go to Sandwalk for another explanation of what telomeres are, why we need them, etc. from a Professor of Biochemistry.
Wednesday, August 5, 2009
Book Recomendation
I just finished Gerd Bantenberg's Egalia's Daughters(amzn). Due to adult situations, (sex, drugs, rock 'n' roll) I'll limit my recomendations to readers over 16. Anyone who has any opinion on feminism and the feminist movement, good or bad, should read Egalia's Daughters.
Monday, May 25, 2009
An Open Letter to Catholic Churchgoers
Dear Catholic Churchgoer,
How many children will need to be raped by priests before you stop
giving your support to the Catholic Church? I would not want to be
associated in the slightest with an organization that has for
years hidden pedophiles within its ranks, never holding them
accountable, but often enabling their vile sins. By not speaking out,
by attending mass, by supporting the Catholic Church, you are
condoning its actions. Shame on you.
For the sake of children everywhere, and for the sake of your own
soul, I'm asking you to stop attending mass and to stop giving money
to the Church until the Vatican makes a full apology and details a
program to correct its actions. I am not asking you to give up your
faith. Pray and read the Bible at home. Attend masses of other
denominations. You can even start a Sunday morning worship group. Do
anything but support the Catholic Church. After all, do you really
want to take spiritual advice from an organization with a documented
60
year history of "endemic" child abuse? The current Catholic leadership cares more about its reputation than your children. How can you trust them with your soul?
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