Wednesday, November 22, 2006

half full?

I was talking to a friend on the phone tonight about various people and their half-full or half-empty approaches to life. After she also described her view I paused and thought for a couple of seconds.

I think I would pour the contents of the glass into a graduated cylinder and measure it. Then I would fill the glass with water, to the brim, and pour that into a second cylinder and measure that. Then I could express as a fairly accurate fraction what the volume had been in the glass compared to capacity. I would also add that it is relative. If the glass only held the original amount, then it would have been full, if the glass held ten times as much then the glass would be mostly empty. Then question those around, “would you choose to have an entirely full glass? One that has an equal amount of free space? or one that is mostly empty, but all three with the same volume?

My answer? If there is a good red wine involved, best if the glass is large and mostly empty, so the wine can breathe.

Wednesday, November 15, 2006

So Cool!

A new genome project is in the works. Technology has advanced to the point that DNA can be recovered from samples that are tens of thousands of years old. Specifically the genome of Homo sapiens neanderthalensis is being analyzed. How closely are they related to us? Do we have any descent from them or not?

As reported by Nicholas Wade in the New York Times

"The archaic human species that dominated Europe until 30,000 years ago is about to emerge from the shadows. With the help of a new DNA sequencing machine that operates with firefly light, the bones of the Neanderthals have begun to tell their story to geneticists.

One million units of Neanderthal DNA have already been analyzed, and a draft version of the entire genome, 3.2 billion units in length, should be ready in two years, said Dr. Svante Paabo, the leader of the research project at the Max-Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Biologists expect knowledge of the Neanderthal genome to reveal, by its differences with the human genome, many distinctive qualities of what it means to be human. Researchers also hope to resolve such questions as whether the Neanderthals spoke, what their hair and skin color were, and whether they interbred at all with the modern humans who first arrived on their doorstep 45,000 years ago, or were driven to extinction without leaving any genetic legacy.

Dr. Paabo has shared some of his precious sample of Neanderthal DNA with Edward M. Rubin of the Joint Genome Institute in Walnut Creek, Calif., whose team has identified 62,250 units of Neanderthal DNA by a different method. The two teams report their results in the journals Nature and Science respectively, saying they have independently demonstrated that recovery of the Neanderthal genome is now possible."

About a million of the estimated 3 billion base pairs have been sequenced, as reported in the Journal Nature

The estimate is that we diverged from them about 500,000 years ago. For many thousands of years both species of man were around.

I was telling everyone who walked into my office.

"It is SOOOO cool!" I said

My students looked at me with a profound lack of interest. Sad.

Imagine what it was like when there were two intelligent species of people at the same time.

Monday, November 13, 2006


We all have different ideas of what exactly is moral and what isn’t. Even within that, who among us measure up to our internal standards? None of us are perfect.

Recently I have found myself thinking frequently of morality, and hypocrisy, and what are the best choices and whether certain belief systems make one more or less prone to deviating from a moral code.


1) Tom Haggard, the pastor of a Christian conservative mega church, who appears to have lied and cheated on his wife with a man who used to be a prostitute. If he hadn’t been so convinced that homosexuality was terribly evil, or that people are weak and tempted by the devil, would this have happened? I was raised a Christian. I remember reading repeatedly in the bible how Jesus valued peace and love, and values poverty and was basically not favorable towards material wealth. I do not remember Jesus saying anything about homosexuals. In spite of this, Christian conservative have no problem with war or wealth, yet hold huge hatred of homosexuality. Many Americans apparently do. Witness the passage of so many state constitutional amendments defining marriage as only between a man and a woman. Why? In my view, whether a gay couple can or cannot get married should only matter to gay couples. And as a biologist I think that monogamy should be encouraged. It reduces the spread of disease, and marriage vows hopefully help encourage monogamy.

I think we need to take responsibility for our own actions. Saying you were tempted is a bad excuse.

2) Speaking of marriage vows and monogamy, I mentioned that Bill Clinton might be an interesting person to have dinner with. He is someone I have always wanted to meet. The person I said that to shuddered in response. I was surprised. President Clinton is a smart man, and charismatic, and concerned about the welfare of the world and the poor and education. I imagine he would be a very very interesting person to talk to over dinner. No, I was told, he is morally reprehensible, and that was that. I was dumbfounded. Yeah, he let an eager woman give him blowjobs, and he shouldn’t have, and he tried to weasel out of admitting it. But I wasn’t talking about DATING him. And yet somehow this tawdry little bit of info, which we would never know about in other people, completely over whelmed any interest in all of the global concerns and projects that Clinton is involved in. Why? Am I some kind of moral idiot to think well of the man for all he has done and said on fronts that are morally important to me because he did something wrong that would cause me to break up with him if I was dating him, or drag him off to a marriage councilor if he was my husband? He did something he shouldn’t have. So did Monica. In my eye they are equally to blame. But among the terrible things one could do, it is not at the top of my list.

The person I had this conversation with is someone I think very highly of. So, now I feel somehow dirtied. Am I wrong? Does one failure taint everything that one does? Even if the failure causes only personal hurt in the family, while good works save lives of thousands? Does my friend screen her dinner companions this way generally? Would she shun artists and musician and philosophers because they had been unfaithful? Have none of her personal friends ever slipped? Are all things equal? Or are they not?

3) A kitten that I sold as a pet last April, a very very sweet and beautiful Blue eyed white Oriental, contracted FIP and was put to sleep a week ago. She lived as an only cat. The virus that killed her likely came from my house, and the genes that made her susceptible to the disease came from one or both of her parents, I own both. As a bit of background, this virus is ubiquitous in places where there are a number of cats, shelters, cat shows, and breeders. Anyone with more than one cat may have a situation with cats passing it back and forth.

The virus is usually harmless. Once in a while, estimated overall at 5% of the time, a cat develops a fatal immune system reaction to the virus and dies. This misfiring of the immune system in response to a mutation in the virus appears to be genetic. A genetic susceptibility. It is the reaction that is FIP, not the virus. Over the decades that I have had cats, I have not had a lot of cases of FIP, and until recently I had sent only 1 kitten out that had contracted FIP and died. In the past 2 years 4 kittens, out of 21 have left my house, only to get FIP some months later. Three of those four went to multi-cat households, but sweet Tink was an only cat.

I have 12 very young kittens in my house. Seven of them are half-siblings of one of the cats that died (10 full sibs are fine and healthy), 5 are nieces and nephews of the same cat. Someone who’s opinion is important to me asked if I was going to keep all the kittens, not sell them or place them, as they stand a chance of getting the disease. I was astonished. One of eleven died. That is one too many, but it is less than 10%. Now I have half sibs and nieces and nephews. Am I worried that they could be susceptible? You bet. Do I think it likely that any individual kitten of this group will get FIP? No. Do I think I should keep these 12 kittens for the rest of their lives in my house because I worry that one or another might be susceptible, or might not be? No. I think it is more fair to the kittens to let them go out and be people’s pets. But because I have been questioned about it I am fretting about it.

I cannot guarantee the life span of any cat that I place. I have had people have cats from me live into their late teens. Others have not made ten. The longest-lived cat on record was a pedigreed cat, but in general I suspect pedigreed cats live somewhat less long on average than moggies. If I had a crystal ball and the right skills, perhaps I could tell someone, THIS cat will live only 8 years, and THAT one will live 18, and you can’t have the pretty one in your lap because she will get FIP and die before she is a year old. But I can’t do that. So I have a guarantee in my sales contract. If the cat dies due to a developmental or hereditary problem, I will replace. That, I can do. My cats are special, they bring joy. They love attention. Should they stay here with only the attention they can get from me? Should I not breed them at all? I try to be careful. I am a geneticist. I do not inbreed, I try to use and produce healthy cats. It is my hobby, and they are a great joy to me.

Am I not moral enough? Most of the time I find myself thinking, “I wouldn’t do that” when some friend or another is telling me what they are doing in some gray area. I try to do the right thing. What should I be doing? What are better choices?

Thursday, November 02, 2006


"The pursuit of truth and beauty is a sphere of activity in which we are permitted to remain children all our lives." - Albert Einstein