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07/09/2009

It's Not the Number of Genes

When last we met, I wrote about memory and about research indicating that, every time we recall a memory, we essentially rewrite that memory when it is returned to the memory vault in our brain. This week (Monday) I received an email from my very good friend Dan in Hawaii. I’ve mentioned Dan a number of times over the years as contributing interesting ideas for these columns. He complimented me on the memory column and I promptly phoned him, not having talked with him for much too long a time. Dan was particularly impressed by an example I cited likening memory to writing on the edge of a deck of cards. After our phone call, I was thinking about a subject for this column and decided that I would revisit light emitting diodes (LEDs), having recently read an article titled "The Dawn of Miniature Green Lasers" by Shuji Nakamura and Michael Riordan in the April issue of Scientific American. 
 
To complement that article, I set out to find another very good article by Nakamura on gallium nitride LEDs in the February Materials Research Society Bulletin. Obviously, my memory deck had been totally shuffled and after several hours searching over a couple of days, I decided that I must have thrown the article out. In self defense, I should note that I got a new desktop computer a week or so ago and had to clear off my desk and surroundings to make way for the components and, as a result, my so-called office is in a state of even more chaos than usual. Finally, on Tuesday, I happened to look on the pull-out shelf housing my new desktop keyboard and there, underneath a couple of booklets that came with the new computer, was the missing Nakamura article. It was less than a foot away from where I had been keyboarding all this time!
 
Well, once I saw the article there was a nagging thought that I’ve written about that paper before. I was certain that I had written about Nakamura, who came up with the gallium nitride blue LED while employed at a small Japanese company. So, I searched the Bortrum archives using our StocksandNews search engine, putting in the words “gallium nitride LEDs” and came up with just one column, dated back in 2000. This was disturbing as I was sure I’d mentioned gallium nitride LEDs more recently. So, I went back to our search engine and put in just the word “LED”. Sure enough, this time I found that I had discussed this very paper less than four months ago, in March of this year! My memory deck was clearly shuffled when it came to this paper.
 
Actually, I’ve had more pressing things on my mind this past week or so. The main concern is a medical problem that my wife developed last week. It’s a problem that seems  relevant in these days of possible action on medical care in the U.S. and illustrates what can happen when an insurer and/or Medicare comes between the doctor and the patient. Back in January, when I switched Medigap plans from one paid for by Alcatel Lucent to another plan costing me over $5K a year, the new plan insisted I switch my blood pressure medication and my doctor put me on lisinopril. I have been taking lisinopril for these past six months without incident.
 
A month or two ago, my wife was also put on lisinopril. A rare side effect of lisinopril, even after prolonged use, can be the development of a severe rash. Wouldn’t you know that last week my wife broke out in a very itchy rash over most of her body and is now on prednisone. She says her recent total knee replacement was a breeze compared to this! I'm mentioning this as a public service should you be one of the many taking lisinopril, as I'm still doing. It's apparently a fine drug unless you're one prone to the rare side effect. (I was not surprised to find that my friend Dan, living the laid back Hawaiian lifestyle, has never had a blood pressure problem in his 85 plus years.)
 
Well, I’ve written several paragraphs and still don’t know what my topic is for this column.  I might as well use a tidbit that I saw in the June 5 issue of Science. A 12-year-old Kansas girl, Clara Ma, is getting a trip to NASA’s Jet Propulsion Laboratory in California, where she’ll sign her name on the next Mars rover, scheduled for launch in 2011. NASA picked the name Curiosity for the rover based on Clara’s letter, one of 9000 proposed names from students around the country. I thought her letter expressed the passion of most scientists quite eloquently:
 
“Curiosity is an everlasting flame that burns in everyone’s mind. It makes me get out of bed in the morning and wonder what surprises life will throw at me that day. Curiosity is such a powerful force. Without it, we wouldn’t be who we are today. Curiosity is the passion that drives us through our everyday lives. We have become explorers and scientists with our need to ask questions and to wonder. ... We will never know everything there is to know, but with our burning curiosity, we have learned so much.”
 
Go, Clara! I imagine that I was about 12 when I got a small microscope and looked at some pond water. If memory serves me correctly, and now you know how dubious that can be, the most impressive little critter in that pond water was a Daphnia. In the same June 5 issue of Science there are reports by Elizabeth Pennisi on items discussed at a meeting in May of this year on “The Biology of Genomes” in Cold Spring Harbor, New York. One of the items discussed was the Daphnia pulex, a crustacean common in ponds all over the world. The Daphnia is a very adaptable creature that can live in salty water, hot water, and/or acidic water. Its eggs can hatch immediately or sit around for a hundred years before hatching. It can clone itself or reproduce sexually; quite a versatile character.
 
Now Daphnia is in the news. I believe at last count our human genome has been found to contain only some 20 to 25 thousand genes. However, tiny Daphnia’s genome contains 31 thousand genes as revealed by a gene-finding program reported at the meeting by John Colbourne of Indiana University. In addition, other work indicates as many as 8,000 more genes missed by the gene-finder. The total of possibly 39,000 genes eclipses the genome of a tiny pest, the pea aphid, with 34,600 genes in its genome. We humans might take offense that these little critters have many more genes than we do. We clearly are more complex creatures than these insects. I'm thinking our complexity involves our "junk” DNA that actually plays key roles turning genes on and off and even telling genes what proteins to code for.
 
But let's get back to the pea aphid. In the past year or so, I’ve seen a number of articles or media reports on the amazing number of bacteria and various microorganisms that inhabit our bodies in mutually beneficial arrangements. The little pea aphid has such a beneficial arrangement with a certain bacterium, Buchnera aphidicola. Let’s call it Buphid for short. The pesky pea aphid, which goes after legumes, sucks up plant sap from the legume. The sap doesn't provide enough protein to satisfy the aphid. Enter Buphid. Buphid, compared to the gene-rich Daphnia or pea aphid, only has about 640 genes; however, some of them are quite important for the aphid. Those genes are responsible for the bacterium making nine amino acids, satisfying the aphid's need for protein supplements. 
 
Normally, you might think that the aphid would have evolved some sort of defense against being infected by bacteria. Not in this case; genes that are active in fighting off bacterial infections are missing. It isn’t a one-way street, however. Leucine is one of the amino acids in question. Surprisingly, the bacterium doesn’t have the enzyme needed to complete the leucine synthesis. It’s found in the aphid , which completes the last step in leucine formation.  The aphid also has imported from another bacterium genes that provide Buphid material to build its cell walls. This back and forth collaboration between the aphid host and its bacterial invader I would imagine must pale in comparison to the many cases of host-invader collaborations going on in our own bodies. It’s a bit scary to think about them.
 
Finally, let’s turn to another facet of genes, in this case with regard to music. Last week I caught the end of a Nova program on TV.  The program was looking at "musicality" and how it differs in various individuals. What intrigued me was the part of the program that I saw dealing with a lady with whom I believe I share a genetic defect! I’m convinced I have this defect that affects my ability to keep time with music. For example, if I’m in an audience which expresses its approval of a performance by clapping together in unison, my wife will tell me to stop clapping - she can’t stand that I’m totally off the beat. My dancing ability, or lack thereof, must be related to what I consider to be my genetic defect.
 
On the Nova Program, there was a lady interviewed who told about her experience with dance class as a young girl. She learned all the steps and could maneuver around the dance floor perfectly; yet, several years later, she was still in the beginners class. She finally realized that she would do the same dance to any music, fast or slow, and was completely out of step with the beat. Today, she’s Irish, she loves going to the pub for the social interactions and applauds the music with the others but never dances. 
 
The item in Science preceding the one on Clara Ma and curiosity was about a genetic study at the University of Helsinki of 343 individuals from 19 Finnish families containing musicians. They found that there was an indication that musicality can be an inherited characteristic. They found a correlation between musicality and a gene that codes for a certain compound, arginine vasopressin, a compound that has also been shown to be responsible for turning promiscuous voles into faithful mates! 
 
The implication is that music promotes attachment behavior. I don’t know if the amazing outpouring of sentiment regarding Michael Jackson’s death is an example of “attachment” by his adoring fans. I think the Finnish study is more along the line that, if music promotes social bonding, music may have played an important role in our own human evolution. 
 
If I finish this column in time, I may well sit down at our piano and try my hand at a tune or two. As you might expect, with my genetic handicap, I tend to play every tune at one tempo - slow! I’ve tried the Minute Waltz but have never attempted to time it. A faithful reproduction of the notes and relative time scale would probably take me an hour, if that! 

Well, between visits to doctors and physical therapists, I’ve managed to fill the space for this column with a variety of topics. If all goes well, the next column will actually have a single theme!
 
Next column on July 23.
 
Allen F. Bortrum
 



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-07/09/2009-      
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Dr. Bortrum

07/09/2009

It's Not the Number of Genes

When last we met, I wrote about memory and about research indicating that, every time we recall a memory, we essentially rewrite that memory when it is returned to the memory vault in our brain. This week (Monday) I received an email from my very good friend Dan in Hawaii. I’ve mentioned Dan a number of times over the years as contributing interesting ideas for these columns. He complimented me on the memory column and I promptly phoned him, not having talked with him for much too long a time. Dan was particularly impressed by an example I cited likening memory to writing on the edge of a deck of cards. After our phone call, I was thinking about a subject for this column and decided that I would revisit light emitting diodes (LEDs), having recently read an article titled "The Dawn of Miniature Green Lasers" by Shuji Nakamura and Michael Riordan in the April issue of Scientific American. 
 
To complement that article, I set out to find another very good article by Nakamura on gallium nitride LEDs in the February Materials Research Society Bulletin. Obviously, my memory deck had been totally shuffled and after several hours searching over a couple of days, I decided that I must have thrown the article out. In self defense, I should note that I got a new desktop computer a week or so ago and had to clear off my desk and surroundings to make way for the components and, as a result, my so-called office is in a state of even more chaos than usual. Finally, on Tuesday, I happened to look on the pull-out shelf housing my new desktop keyboard and there, underneath a couple of booklets that came with the new computer, was the missing Nakamura article. It was less than a foot away from where I had been keyboarding all this time!
 
Well, once I saw the article there was a nagging thought that I’ve written about that paper before. I was certain that I had written about Nakamura, who came up with the gallium nitride blue LED while employed at a small Japanese company. So, I searched the Bortrum archives using our StocksandNews search engine, putting in the words “gallium nitride LEDs” and came up with just one column, dated back in 2000. This was disturbing as I was sure I’d mentioned gallium nitride LEDs more recently. So, I went back to our search engine and put in just the word “LED”. Sure enough, this time I found that I had discussed this very paper less than four months ago, in March of this year! My memory deck was clearly shuffled when it came to this paper.
 
Actually, I’ve had more pressing things on my mind this past week or so. The main concern is a medical problem that my wife developed last week. It’s a problem that seems  relevant in these days of possible action on medical care in the U.S. and illustrates what can happen when an insurer and/or Medicare comes between the doctor and the patient. Back in January, when I switched Medigap plans from one paid for by Alcatel Lucent to another plan costing me over $5K a year, the new plan insisted I switch my blood pressure medication and my doctor put me on lisinopril. I have been taking lisinopril for these past six months without incident.
 
A month or two ago, my wife was also put on lisinopril. A rare side effect of lisinopril, even after prolonged use, can be the development of a severe rash. Wouldn’t you know that last week my wife broke out in a very itchy rash over most of her body and is now on prednisone. She says her recent total knee replacement was a breeze compared to this! I'm mentioning this as a public service should you be one of the many taking lisinopril, as I'm still doing. It's apparently a fine drug unless you're one prone to the rare side effect. (I was not surprised to find that my friend Dan, living the laid back Hawaiian lifestyle, has never had a blood pressure problem in his 85 plus years.)
 
Well, I’ve written several paragraphs and still don’t know what my topic is for this column.  I might as well use a tidbit that I saw in the June 5 issue of Science. A 12-year-old Kansas girl, Clara Ma, is getting a trip to NASA’s Jet Propulsion Laboratory in California, where she’ll sign her name on the next Mars rover, scheduled for launch in 2011. NASA picked the name Curiosity for the rover based on Clara’s letter, one of 9000 proposed names from students around the country. I thought her letter expressed the passion of most scientists quite eloquently:
 
“Curiosity is an everlasting flame that burns in everyone’s mind. It makes me get out of bed in the morning and wonder what surprises life will throw at me that day. Curiosity is such a powerful force. Without it, we wouldn’t be who we are today. Curiosity is the passion that drives us through our everyday lives. We have become explorers and scientists with our need to ask questions and to wonder. ... We will never know everything there is to know, but with our burning curiosity, we have learned so much.”
 
Go, Clara! I imagine that I was about 12 when I got a small microscope and looked at some pond water. If memory serves me correctly, and now you know how dubious that can be, the most impressive little critter in that pond water was a Daphnia. In the same June 5 issue of Science there are reports by Elizabeth Pennisi on items discussed at a meeting in May of this year on “The Biology of Genomes” in Cold Spring Harbor, New York. One of the items discussed was the Daphnia pulex, a crustacean common in ponds all over the world. The Daphnia is a very adaptable creature that can live in salty water, hot water, and/or acidic water. Its eggs can hatch immediately or sit around for a hundred years before hatching. It can clone itself or reproduce sexually; quite a versatile character.
 
Now Daphnia is in the news. I believe at last count our human genome has been found to contain only some 20 to 25 thousand genes. However, tiny Daphnia’s genome contains 31 thousand genes as revealed by a gene-finding program reported at the meeting by John Colbourne of Indiana University. In addition, other work indicates as many as 8,000 more genes missed by the gene-finder. The total of possibly 39,000 genes eclipses the genome of a tiny pest, the pea aphid, with 34,600 genes in its genome. We humans might take offense that these little critters have many more genes than we do. We clearly are more complex creatures than these insects. I'm thinking our complexity involves our "junk” DNA that actually plays key roles turning genes on and off and even telling genes what proteins to code for.
 
But let's get back to the pea aphid. In the past year or so, I’ve seen a number of articles or media reports on the amazing number of bacteria and various microorganisms that inhabit our bodies in mutually beneficial arrangements. The little pea aphid has such a beneficial arrangement with a certain bacterium, Buchnera aphidicola. Let’s call it Buphid for short. The pesky pea aphid, which goes after legumes, sucks up plant sap from the legume. The sap doesn't provide enough protein to satisfy the aphid. Enter Buphid. Buphid, compared to the gene-rich Daphnia or pea aphid, only has about 640 genes; however, some of them are quite important for the aphid. Those genes are responsible for the bacterium making nine amino acids, satisfying the aphid's need for protein supplements. 
 
Normally, you might think that the aphid would have evolved some sort of defense against being infected by bacteria. Not in this case; genes that are active in fighting off bacterial infections are missing. It isn’t a one-way street, however. Leucine is one of the amino acids in question. Surprisingly, the bacterium doesn’t have the enzyme needed to complete the leucine synthesis. It’s found in the aphid , which completes the last step in leucine formation.  The aphid also has imported from another bacterium genes that provide Buphid material to build its cell walls. This back and forth collaboration between the aphid host and its bacterial invader I would imagine must pale in comparison to the many cases of host-invader collaborations going on in our own bodies. It’s a bit scary to think about them.
 
Finally, let’s turn to another facet of genes, in this case with regard to music. Last week I caught the end of a Nova program on TV.  The program was looking at "musicality" and how it differs in various individuals. What intrigued me was the part of the program that I saw dealing with a lady with whom I believe I share a genetic defect! I’m convinced I have this defect that affects my ability to keep time with music. For example, if I’m in an audience which expresses its approval of a performance by clapping together in unison, my wife will tell me to stop clapping - she can’t stand that I’m totally off the beat. My dancing ability, or lack thereof, must be related to what I consider to be my genetic defect.
 
On the Nova Program, there was a lady interviewed who told about her experience with dance class as a young girl. She learned all the steps and could maneuver around the dance floor perfectly; yet, several years later, she was still in the beginners class. She finally realized that she would do the same dance to any music, fast or slow, and was completely out of step with the beat. Today, she’s Irish, she loves going to the pub for the social interactions and applauds the music with the others but never dances. 
 
The item in Science preceding the one on Clara Ma and curiosity was about a genetic study at the University of Helsinki of 343 individuals from 19 Finnish families containing musicians. They found that there was an indication that musicality can be an inherited characteristic. They found a correlation between musicality and a gene that codes for a certain compound, arginine vasopressin, a compound that has also been shown to be responsible for turning promiscuous voles into faithful mates! 
 
The implication is that music promotes attachment behavior. I don’t know if the amazing outpouring of sentiment regarding Michael Jackson’s death is an example of “attachment” by his adoring fans. I think the Finnish study is more along the line that, if music promotes social bonding, music may have played an important role in our own human evolution. 
 
If I finish this column in time, I may well sit down at our piano and try my hand at a tune or two. As you might expect, with my genetic handicap, I tend to play every tune at one tempo - slow! I’ve tried the Minute Waltz but have never attempted to time it. A faithful reproduction of the notes and relative time scale would probably take me an hour, if that! 

Well, between visits to doctors and physical therapists, I’ve managed to fill the space for this column with a variety of topics. If all goes well, the next column will actually have a single theme!
 
Next column on July 23.
 
Allen F. Bortrum