Saturday, December 31, 2005
Sleeping in and Lorikeets
12-31-2005 We are in the Florida mode. There is no reason to get up early. Our dog is in the kennel up north so it isn’t wandering around the bedroom tinkling its bell asking to be let out and especially to be fed. The horses are also up north so there is no guilt being felt by delaying the hay and grain. We all trundled off to the new Naples garden center which also had butterflies, lizards, and lorikeet birds. One Lorikeet hoped on my nice and didn’t want to leave. After some effort we moved it to my nephew and then to the bird keeper. It just seemed to want to sit on someone. Then it was back for a swim in the Gulf followed by the pool and Jacuzzi. Much of the time was taken up by playing tag with my nephew and nice who seemed to have an in exhaustible source of energy. Their favorite game was drown the uncle.
We had baked brie and chips and salsa for appetizers washed down with margaritas. Then we all trooped out to the lawn on the Gulf to watched the Naples fireworks. This strategy avoided the mess near the pier but the fireworks were somewhat distant. Also, the wind was slight with the smoke hanging over the town pier obscured many of the displays. Anyway, it was fun. Tim and I then cooked steaks on the grills by the west pool. For our own steaks we applied substantial amounts of garlic salt and chili powder but in an act of kindness left these condiments off those for the rest of the family. After a great meal and good wine we played the card game bluff till midnight. We used two decks of cards. I was caught on one of my bluffs and ended up with the majority of two decks in my had as the discard pile was rather large at the time of my demise.
Friday, December 30, 2005
Swiming in the Gulf and Cloyde's
12-30-2005 The Gulf was cold, about 65 degrees, but Ben, Sola, Tim and I ventured into the salty water. All of us made the “up to the neck” club as with time the body numbs up and you don’t notice that your peripheral circulation is shutting down. I came out and hopped in the Jacuzzi only to have my fingers start to tingle as the circulation returned to the more distant portions of my body. In the late afternoon we all got dressed up and ventured out to Cloyde's Steak & Lobster House in the “Village” a couple of miles north of the condo for their early bird special. At this time of year you have to hit a half hour window to get the early bird. The portions are smaller than later but really are just about the right size.
Thursday, December 29, 2005
Brother in law arrives
Wednesday, December 28, 2005
Walking and Intelligent Design.
There is much being said in the local paper about intelligent design. I do not believe that the subject belongs in science classes but do believe that it is appropriate for the study of history, government and philosophy. The incompatibility comes from the fact that science does not allow miracles but religion requires them.
It is interesting to speculate on the possibility of creating an Earth that inyoung but looks old as demanded by Intelligent design. As we gain in technological expertise, it is becoming more and more possible to do just that. Using today’s technology we could fool people who lived one hundred years ago by placing bones of the proper composition in the proper setting. We might even be able to fool scientists from 50 years ago by using the proper isotopic ratios making the material look old to the sophisticated chemist of that time. Just imagine what people a few hundred years in the future could do to fool us. There is even work to create the first synthetic organism. Although it will be only a lowly mycoplasma, the proof of principle will have been accomplished. While we will soon be able to perform intelligent design on our own; our future abilities do not prove that and intelligent designer was active in the past. In fact, with our new ability to see the structure of the genome of many organisms in detail and plot the progress of evolution, it does not look well designed at all. Our genome is quite a mess, nothing that an intelligent designer would create. It looks just like something produced by random mutation followed by natural selection.
Tuesday, December 27, 2005
The Dock in Naples Fl
Naples Dinner Theater
Gaia, Fishing and Christmas in Naples
It has been a wonderful Christmas in warm sunny Naples Florida. We are at my mother in laws staying in a beautiful condo on the Gulf of Mexico with my wife, mother and more family to come later. The food has been great and I received several books on science as presents including Lovecock’s latest rendition of his original book on Gaia. I am a believer in Gaia or that all the biology of Earth forms a single mega-organism. Often, commuting down route 128 I have felt like a mindless corpuscle being swept along as a small part of some gigantic organism. We are ourselves composed of billions of relatively independent living organisms. Although the environments are artificial, each can live independently of our body in the proverbial Petri plate. So why not accept the mega organism Gaia which is also composed of individual organisms all working together to make the Earth compatible with existing life? There is considerable evidence that for over 2 billion years life has been altering the environment to keep it compatible with living organisms. The Earth is chemically out of balance and kept that way be living organisms. There are many concerns today about our effect on the environment and our pushing it away from some “natural” state. Pushing the environment away from some “natural” sate is what life has been doing for the last 2 billion years. I am not for every change our species has wrought on the Earth but we should be careful that our environmentalism doesn’t create more problems than it solves. In Brazil there has been a push for ancient slash and burn farming rather than modern fertilizer based agriculture. This has resulted in thousands of ancient species being eliminated by destruction of the ran forest. It would have been better to farm less land intensively and left the rain forest alone.
Yesterday I was out on the Gulf with 20 other people supposedly deep sea fishing. No fish was hurt. Not a one of us caught anything and some lost. The sea was very rough with swells higher than the boat. Our trip out was directly reminding me of past experiences on horses who were intent on my removal. Our deranged captain was providing a ride similar to that on a bucking bronco. It was amazing that the guy next to me could throw up so much and for so long. Counting the bait that was lost and the digestive juices expelled, we put more in than we took out. The fish had nothing to fear. I did see one large sea turtle but other than the pelicans and sea gulls, no other sea life.
Sunday, December 25, 2005
Christmas in Naples
12-25-2005 We had a pleasant Christmas in Naples with gift unwrapping in the morning and the turkey dinner in the afternoon. It was great especially the candied sweat potatoes. I received several books on cosmology. All the girls go holiday shirts. Many thanks to Vesta for having us all down to the condo.
Wednesday, December 21, 2005
Intelligent design defeated - Getting ready to fly South
From Pennsylvania judge and CNN "We have concluded that it is not [science], and moreover that ID cannot uncouple itself from its creationist, and thus religious, antecedents," Jones writes in his 139-page opinion posted on the court's Web site.
On the home front, the furnace cleaning guy made it this cold but clear morning. We are leaving for the South tomorrow and were worried that his visit would be postponed. At this time of year one wants to make sure that things are working as well as possible. He said that our furnace was in superb shape. Such a glowing evaluation of our heating system makes me nervous.
Last year we installed a temperature monitor that calls us if our homes internal temperature drops below 45 degreed F. You can also call the machine for an update including the status of its back-up battery. We are also having people take care of the horses and check out the house on a daily basis. One lady may even stay a few days. Hopefully, the parties will leave the house relatively intact.
I am taking my laptop on the trip but my mother-in-law doesn’t have an internet hookup. But not to worry as I can hook the laptop up to my cell phone. On giving the system a try and it promptly crashed my computer. I thought Microsoft XP would not crash. After about two hours on the phone with the people from Verizon we got it working. The solution was to delete various parts of their software until the computer didn’t crash when the communication software was activated. Another try today showed the system working well but slowly. It only chugs along at 14.4k baud. My first modem communicated at 0.3k baud. Although very slow one could read incoming text as it crept across the screen. Back then there was no such thing as graphics. So, even 14.4k baud is not so bad, especially as I have a ton of unused minutes.
Tuesday, December 20, 2005
Where did you come from - National Geographic Genographic
Last night I signed up to be sampled for a human genome study sponsored by National Geographic and IBM https://www5.nationalgeographic.com/genographic/index.html?fs=www9.nationalgeographic.com .
They will send a sampling kit, then analyze the cheek swab samples and provide data on geographical location of one’s ancestors. I believe that they are using mitochondrial and Y chromosome DNA so that they can look at both maternal and parental lines. I have a friend who claims to be an American Indian and I am trying to get him to sign up to see if he is telling the truth. The kit costs $100 and I assume that some of the proceeds go to fund sampling in other parts of the world.
The following is from their site:
The National Geographic Society, IBM, geneticist Spencer Wells, and the Waitt Family Foundation have launched the Genographic Project, a five-year effort to understand the human journey—where we came from and how we got to where we live today. This unprecedented effort will map humanity's genetic journey through the ages.
The fossil record fixes human origins in Africa, but little is known about the great journey that took Homo sapiens to the far reaches of the Earth. How did we, each of us, end up where we are? Why do we appear in such a wide array of different colors and features?
Such questions are even more amazing in light of genetic evidence that we are all related—descended from a common African ancestor who lived only 60,000 years ago.
Though eons have passed, the full story remains clearly written in our genes—if only we can read it. With your help, we can.
When DNA is passed from one generation to the next, most of it is recombined by the processes that give each of us our individuality.
But some parts of the DNA chain remain largely intact through the generations, altered only occasionally by mutations which become "genetic markers." These markers allow geneticists like Spencer Wells to trace our common evolutionary timeline back through the ages.
"The greatest history book ever written," Wells says, "is the one hidden in our DNA."
Different populations carry distinct markers. Following them through the generations reveals a genetic tree on which today's many diverse branches may be followed ever backward to their common African root.
Our genes allow us to chart the ancient human migrations from Africa across the continents. Through one path, we can see living evidence of an ancient African trek, through India, to populate even isolated Australia.
But to fully complete the picture we must greatly expand the pool of genetic samples available from around the world. Time is short.
In a shrinking world, mixing populations are scrambling genetic signals. The key to this puzzle is acquiring genetic samples from the world's remaining indigenous peoples whose ethnic and genetic identities are isolated.
But such distinct peoples, languages, and cultures are quickly vanishing into a 21st century global melting pot.
That's why the Genographic Project has established ten research laboratories around the globe. Scientists are visiting Earth's remote regions in a comprehensive effort to complete the planet's genetic atlas.
But we don't just need genetic information from Inuit and San Bushmen—we need yours as well. If you choose to participate and add your data to the global research database, you'll help to delineate our common genetic tree, giving detailed shape to its many twigs and branches.
Together we can tell the ancient story of our shared human journey
Monday, December 19, 2005
We left the chimps long ago
New studies show that we and chimps had a common ancestor between 5 to 7 million years ago. This estimate is thanks to Blair Hedges, an astrobiologist at Penn State. The only challenge to this would be my own experience. I am sure that several of my college fraternity brothers diverged from chimps much more recently. What to you think?
My Christmas shopping is almost done and we are soon to fly south to Florida. If my cell phone modem works I hope to continue this blog through the Holidays.
Merry Christmas to all
Sunday, December 18, 2005
The English are crazy - Kill a Badger, Save a Cow?
The English are a strange group. They recently outlawed the killing of foxes via fox hunting and now they want to kill off European badgers. Save a fox and kill a badger. The rational is that these badgers carry TB and can transmit it to cattle which has been a major problem in the past. Trials have been done and in some cases, the transmission to cattle actually increased after the badgers in an area were killed. The explanation is that when badgers in one area were killed those in adjacent areas roamed more widely and infected more cattle. The cattle farmers take this result as proof that they should get all the badgers so that there are none left to roam. The environmentalists say that the results show that culling will not work. What will the English do? They will keep a stiff upper lip and do something absurd.
Saturday, December 17, 2005
A walk in the woods; the evolution of dogs and the future of humans
I was reading about the dog genome and estimates that they were domesticated tens of thousand of year ago. The canines have been with us for a long time and it is sobering that we have changed their configuration so much in such a short time. This is one plastic genome. What will happen in our future as we gain the ability to modify our own genome for cosmetic purposes? Will blonds predominate? Will the average bust size increase? Will we have hermaphrodite appear with both male and female genitalia? Some gays are trying this through surgery today. It will soon be possible to create true test tube babies freeing women forever from the pain and discomfort of child bearing. This will allow women to drink and get stoned without affecting their fetus developing in a distant laboratory. Will convenience win? Where will it go?
Thursday, December 15, 2005
Skiing on a cold but beautiful day and motion sensitive lights
Wednesday, December 14, 2005
Bears for children in distress and State Police
Today at our Rotary meeting, we collected teddy bears and the odd Snoopy for the State Police. Each officer keeps one in their cruiser for young children that they may encounter in the line of duty that need comforting. The receiving officer who attended the meeting is a ex-marine who we met at the Fox Hunt. She is also in the mounted patrol. Our club has provided bears before but I believe that this is the first time that an officer was present to accept them.
Tuesday, December 13, 2005
Find that dog – Dog tracking collars
Friends are looking into radio transmitting dog collars. When out hunting hounds can really go and forget about their position in this life, property of us humans. When they are on the sent nothing else matters. These things cost about $1500 for a receiver and two collars. Battery life and moisture sensitivity are also issues. It is interesting that some collars will transmit whether the dog is moving, barking or has something up a tree.
GPS systems are also available but require the use of a GSM cell phone to interrogate the GPS unit and a clear view of the sky so 4 satellites are always in view. My personal experience with GPS in the forest is that the signal is often lost due to trees and gullies. Also, the less expensive ones just give a position by latitude and longitude that have to be translated into a position by some other means. Software programs exist to do this but one would have to go running thought the woods carrying a laptop. There are some systems that will call your GSM phone when the dog go outside of set boundaries such as out of your yard. It seems to me that there is an application here for tracking teenagers.
Monday, December 12, 2005
Snowshoeing in the town forest
Sunday, December 11, 2005
Littleton Horse Owners Christmas Party and a Hanging Moose
Saturday I attended the LHOA Christmas Party at a local Chinese restaurant. It is always at a Chinese restaurant and as my wife doesn’t like Oriental food it is the only time that we go to such a restaurant. They always have a Yankee swap where one picks a number and chooses a gift in turn. The gift must be opened for all to see and you have a chance to exchange your gift for someone else’s. It is best to be first because at the end you can choose any gift. Second is worst as you only have one gift to choose from. I was 14th which is not a bad position. My gift was a lead rope which for some reason I traded for a Moose wall hanging (see photo). When my wife’s turn came she traded her gift, a ceramic holiday figure that would have to dusted, for the lead rope. I apologize to the guy who had both of use steal a gift from him. This club is big on awards and I got one for showing up (see photo). Some sage once said that 90% of life is just showing up.
Saturday, December 10, 2005
Rotary and the Salvation Army
Today I did my part as a Rotarian helping to ring the Salvation Army bell at a local grocery. We also gave out free candy. People gave us money and we gave them tooth decay and diabetes. Most folks were very nice and we had a full pot. A lady came by and exchanged our full pot for an empty one. I hope that she really worked for the Salvation Army. Al least she had the right type of pot.
Friday, December 09, 2005
A snowy day with time to think about evolution and Sigma Xi
Fluffy white snow is quietly falling outlining our dark split rail fence. The pasture beyond is covered in a blanket of white with the brown woods beyond. I am in my office enjoying the view.
We have not been able to receive telephone calls for about a day. One can dial out but the phone rings once and hangs up on incoming calls. Fortunately, we have cell phones. Verizon is sending someone between 8:00am and 6:00 pm; that is if they can get through the snow.
This morning my Email contained a note from Sigma Xi, the honorary society for those who author scientific papers. I have been a member for about 30 years. It also lobbies on issues that affect the practice of science and some of the latest efforts are presented on the link below. The URL contains links to articles in American Scientist on topics related to evolution and the intelligent design controversy. It is a good resource.
http://www.sigmaxi.org/resources/evolution/index.shtml
Thursday, December 08, 2005
It is very cold in Massachusetts – How do horses and plants cope?
Our horses are very fuzzy as their hair is standing on end to reduce air convection extending their bio insulation layer. We hairless humans have lost that ability. How do plants keep from freezing?
I found the following on the web.
Brrrr! How do outdoor plants avoid freezing to death? Not being able to don gloves and a scarf, or shiver, to keep warm, it's a wonder that trees and shrubs aren't freezing to death outside. Sometimes, of course, they do. But usually that happens to garden and landscape plants pushed to their cold limits, not to native plants in their natural habitats. Think about it: Water freezes at 32 degrees Fahrenheit, not a particularly cold temperature for a winter night, and plants contain an abundance of water. Water is unique among liquids in that it expands when it freezes, so you can just imagine the havoc that would be wreaked as water-filled plant cells froze and burst. Nonetheless, hardy trees and shrubs survive temperatures well below freezing each winter, and those of boreal regions live where temperatures dip below even minus 150F. Water, whether in a plant cell or a glass, does not always freeze when chilled below 32F. To freeze, water molecules need something around which to begin grouping to form ice crystals, a so-called nucleating agent. Without a nucleating agent, water will "supercool" and remain liquid to about minus 40F, at which point ice forms whether or not a nucleating agent is present. All sorts of things can serve as nucleating agents – bacteria, for instance – so plants may not be protected all the way down to minus 40F by having their water supercool. But winter temperatures don't plummet that low over much of the temperate region, so just a bit of supercooling may be all a plant needs to survive winter cold. Plants have another trick for dealing with the cold, one that is effective well below that minimum supercooling temperature. That trick is to let water freeze only outside their cells, where the ice won't cause damage. Cell membranes are permeable to water, so as temperatures drop ice crystals that form outside plant cells grow with the water they draw from within the cells. The plant is now threatened more by dehydration than by freezing. One other thing at work for the plants here is something called freezing point depression, a term you may remember from high school chemistry. Basically, whenever you dissolve something in water, you lower the resulting solution's freezing point, more so the more that's dissolved. Plant cells are not pure water, and as the liquid in those cells losing water becomes more and more concentrated, the cells' freezing point keeps falling. The plant is not a passive player in this cold story. In preparing for cold, cell walls strengthen and sugars that concentrate in the cell sap are produced, as are compounds that alter cell permeability to water. And here is where we gardeners can step in. Light supplies the energy that plants need to prepare for cold, so we can make sure to locate and prune plants so they get adequate light. Fruits are energy sinks, so we can also make sure not to overcrop a plant, especially one that is borderline hardy. Besides preparing plants for the cold, we can play around with microclimate, the climate right around a plant. Plants near south-facing walls, near paving or sheltered from north winds keep a few degrees warmer than their more exposed counterparts. Swaddling a plant for winter, such as is often done with roses, does nothing for its appearance but does give it a few extra degrees of warmth. A plant needs to experience some cold before it can undergo those previously mentioned changes with which it prepares for cold, so never swaddle a plant too soon in autumn. Unfortunately, all this fiddling with a plant to help it through winter palls in the face of genetics. The very most that we gardeners can do to help trees and shrubs face winter is to plant those that naturally tolerate the amount of cold our winters are apt to serve up. Around here, plan on winter temperatures plummeting to about minus 20F. Lee Reich, a New Paltz horticulturist, writes a weekly garden column for the Times Herald-Record. Feel free to e-mail questions to springtown@netstep.net and he'll answer them directly or in this column. His Web site is www.leereich.com.
Tuesday, December 06, 2005
What is a “theory” – cosmology, intelligent design and string theory
Lawrence Krauss, a professor of physics at Case Western Reserve University, has an article in the Dec. 3 2005 issue of New Scientist (http://www.newscientist.com/) called “Mind your language”. In it he says “A scientific theory is a logically coherent and predictive system that has been tested against experiment or observation”. Thus, since the string “enterprise” has not produced predictions that can be verified by experimentation, it is not a theory. This definition of “Theory” gets around the complaint of Intelligent Design folks who say that evolution is just a theory implying that it has not been verified. Of course it has been verified. Krauss’s definition of the word “Theory” includes verification and could only be used with ideas that have been substantiated by experimentation. Thus, the string “enterprise” or intelligent design “enterprise” would not be theories. This is not common usage and is confusing. It seems to me that using the phrases proven or substantiated theory would be a better means of indicating verification than just the word by itself. To most people the word theory does connote something that is conjecture. It may be a conjecture that has been substantiated through experimentation, has been refuted through experimentation or not rigorously evaluated. Come to think of it, it seems to me that the word conjecture would be best for unproven theories. Conjecture seems to emphasize the lack of proof or substantiation. Perhaps we should have conjectures and proven conjectures and stop using the word “theory” all together as its definition has become so muddled.
By the way, I have asked Santa Claus to bring me Krauss’s new book, “Hiding in the Mirror”
Saturday, December 03, 2005
Age over youth
"You grew up in a different world," the student said, loud enough for everyone around them to hear. "Today we have television, satellite positioning, jet planes, and space travel; men have walked on the moon; our spaceships have visited Mars; and we even have nuclear energy, electric and hydrogen cars, cell phones, and computers with high-speed processing."
Taking advantage of a pause in the student's litany, the geezer said, "You're right. We didn't have these things when we were young, so we invented them, you little twit. What are you doing for the next generation?"
I love senior citizens!
The chemistry of Drag Fox Hunting
I searched through my “Perry’s” which was the chemical engineer’s bible in my day. A close organic compound to your anise oil in terms of boiling point was nicotine. Nicotine boils at 247C and anise oil boils at 238C (460F). The vapor pressure/temperature profile for nicotine follows as (vapor pressure in mmHg/temp degrees C): 1/62, 5/92, 10/107, 20/124, 40/142, 60/155, 100/170, 200/194, 400/220, 760/247. Normal graph paper is useless for plotting this for your temperature range so I would try semi-log paper which I do not have. Maybe you could extrapolate down to your temperature region to guess at the change in vapor pressure between 77F (25C) and 32F (0C).
I also looked at organic compounds that had vapor pressure data for your temperature range; that is, from 25C down to 0C. Here is that data:
Degrees C Degrees C Degrees C
V.P. mmHg N-nonane N-butyl Pentachloro-
Ketone ethane
1 1.4 -1.4 1.0
5 25.8 19.7 27.2
It appears that many organic compounds undergo a 5-fold drop in vapor pressure between 25C and zero C. If I were working your problem I might conclude I had to increase the concentration of anise oil 5-fold to get the same vapor pressure at zero C as at 25C.
I sure am glad I no longer have to earn my living by my expertise in chemistry and vapor pressures. Good luck.
Thursday, December 01, 2005
Wednesday, November 30, 2005
Ericson sailboat on the hard in Maine getting ready for winter
Today I drove up to Maine to visit my boat. It gets lonely if you don’t visit it every so often. They pulled the boat a couple of weeks ago so it is on stanchions on the “hard” (the ground). Part of the wood frame for the shrink wrap was up and the workmen said that they would have it wrapped in the next few days. There are always pluses and minuses with regard to the boats position. Last year it was inland a couple of rows giving it good protection from the wind, especially during the Spring commissioning, but was very close to another boat making hull work difficult. This year it is on the edge of the bay but has good room between it and the boats on either side, which will make hull work easier if the wind is not too stiff. It ain’t warm in Maine in the Spring. The folks at the yard said that shrink wrap plastic is now available. Earlier it was in short supply due to need for the same plastic to make siding for hurricane repairs. Hopefully the old boat will soon be shrink-wrapped and they will place the door in a location that makes entrance and exit doable with excessive contortions. Last year you had to be a pretzel to get on and off the boat through the shrink wrap.
Monday, November 28, 2005
An important problem for chemists and physicists
Anise is used as a scent for hounds to follow in various sports. We lay the scent by squirting a few drops of the mixture every ten steps on the surrounding biosphere. A small amount of anise oil is added to vegetable oil as a vehicle. The vegetable oil is a good solvent for the anise oil and helps it stick to the plant life. This formulation has remained constant through the year but the hounds seem to be able to scent better in warmer weather. It is my contention that in cooler weather the anise oil is less volatile resulting in a lower vapor density making it less sniffable by the hounds. If our formulation is optimal for 70 degrees F, how much more anise should we add so that density of anise in the air will be the same at 35 degrees F? Any help would be appreciated. By the way, I don’t want references to text books or tables but an answer such as add 5 times as much anise at 35 degrees.
Thanks for your help
Saturday, November 26, 2005
Intellegent design and string theory
Friday, November 25, 2005
Aging, Progeria and farnesyl – there is new hope
I have discussed Progeria before. This is a most unfortunate inherited disease in which children appear to age prematurely. They often die by the age of 13 due to atherosclerosis (heart disease). More information can be found at the web page of the Progeria Research Foundation (http://www.progeriaresearch.org/index.shtml ), which has its own interesting history and is a major force in Progeria research. A recent scientific publication listed at http://www.progeriaresearch.org/index.shtml shows the link between a modification of the protein lamin A and a cholesterol precursor, farnesyl phrophosphate. The chemical structure is shown below.
Genetic studies have previously shown that a mutation in the lamin A gene is responsible for this disease. Lamin A is a cellular structural protein. The mutated form causes aberrant nuclear morphology and probably other biochemical dysfunctions. After the lamin A protein has been synthesized in the cell it is modified by the addition of a farnesyl moiety and methylation. A section of the protein containing these modifications is removed by the action of an enzyme (Zmpste24) that acts at a specific site in the lamin A protein. The Progeria mutation eliminates the region of lamin A containing the enzyme binding site so that the enzyme can’t remove the modified portion of lamin A. This lack of sequence specific proteolysis results in a lamin A with the farnesyl still attached. Even in the presence of normal lamin A, the aberrant form containing farnesyl will cause nuclear deformities and the symptoms of Progeria. It is interesting that farnesyl is also implicated in osteoporosis and cancer. A drug (Tipifarnib) that inhibits the enzyme farnesyl transferase keeping farnesyl off proteins such as lamin A is in phase III clinical trials (http://www.clinicaltrials.gov/ct/show/nct00093418 ) as a treatment for certain types of leukemia.
Will such a drug be able to cure or reduce the symptoms of Progeria?
Could this drug even slow down normal aging? Stay tuned.
Wednesday, November 23, 2005
The Gaia Hypothesis - How would the Earth reproduce
What is an organism? It is an assemblage of living parts that are contiguous and interdependent. This definition includes us. Such organisms may reproduce by fissinoning into existing and new entities that become physically separate or it may simply continue to exist as a single entity. Most of the organisms that we encounter reproduce by creating a new entity that is physically separate but this is not required. Why does a living entity need to create new entities? One can easily imagine a single living entity made of living parts that are created and destroyed as time progresses. This process would renew and rejuvenate the living entity without requiring division into a second entity. As I have discussed before, our bodies are continually being regenerated. Although we eventually die, we only live as long as we do because of this continual regeneration. Genetic defects such as those in the genetic disease progeria inhibit this rejuvenation resulting in rapid aging and tragically shortened lifetimes. With continual and perhaps more effective rejuvenation an entity could live on without dividing and creating a separate organism. The Earth could be such a living but non-dividing organism. How could the Earth reproduce? It would be difficult for the Earth to divide by fission but it certainly can bud off parts of its biosphere, something like a big yeast. We could be the reproductive mechanism of the Earth when we establish a biosphere off the globe.
Tuesday, November 22, 2005
The Anthropic Cosmological Principle by Barrow and Tipler
Well, I have just finished this 677 page tome which includes a large number of differential equations and poorly defined words. It is written for cosmologists and is not for the casual reader. I am not a cosmologist by profession but am intrigued by the questions raised by this pursuit and while know something about differential equations, don’t know enough to truly appreciate many of the arguments presented by the authors. This book asks why the constants of nature are so nicely set as to allow our existence. If many of them were just a little different then life as we know it could not exits. If gravity were just a little stronger all would be black holes. If the charge on an electron were just a little weaker then molecules would not form. The weak anthropic principle (WAP) says that things are so good for us because if they were different we wouldn’t be here to ask the question. The strong anthropic principle (SAP) says that some one or some thing made the universe this way so that we would exist. There is also the “final anthropic principle” (FAP) which says that intelligent information-processing must come into existence in the Universe, and, once it comes into existence, it will never die out.
At the conclusion of the book arguments are presented for life taking over the entire universe and possibly avoiding eventual collapse into the big crunch. It seems that current thinking has the universe expanding forever due to the newly discovered dark energy avoiding the big crunch altogether. The authors Borrow and Tipler published this book in 1986 so it is a little out of date. In 1986 most thought that the universe would eventually collapse in the big crunch as described in this book. It is interesting that so many people are spending so much time trying to figure this out. Most of the time scales are billions of years in the future and of little consequence to us today. However, it is fun to conjecture on Government money.
The final diagram from the book includes the Omega Point of Tipler - The Tipler Scenario: Life expands to fill the universe, which is closed. As it begins to contract, life uses its shear energy to survive and manipulate its evolution. As the universe collapses, the speed of information processing increases without bound and life evolves into an Omega Point.
Sunday, November 20, 2005
Fox Hunting and Flying
Yesterday I participated in another fantastic fox hunt through woods and fields a few miles from my home. I am a fox. It is wonderful that this region has so many conservation areas that protect the natural environment. Our local is developing rapidly and if the conservation groups weren’t active there would be little undeveloped land left in a few years. My wife led the field on her most experience jumper. The weather has been great so that horse has been getting quite a workout in the last few weeks.
Today a friend offered to take me for a ride in his plane. The weather was bright but cool providing for extensive visibility. We could easily see Mt. Monadnock in the distance. They directed the plane over my home and circled a few time so I could get some pictures. Our white horse looked a little nervous standing perpendicular to the sun for maximal exposure to the sun’s rays. Who says that horses aren’t adept at physics? I took some pictures with my little camera which only generates 3 megabyte pictures. My friend’s camera shoots 16 meg images. It can take highly detailed photos that are comparable to those taken on film even when printed in large format. It has been a long time since I have been up in a small plane and I really enjoyed the experience.
Friday, November 18, 2005
Capote
Today I saw the film Capote. It was excellent but probably not a blockbuster. It seems to be showing at a limited number of theaters in the area. One interesting aspect was the comparison between Capote and one of the murderers chronicled in his book “In Cold Blood”. They had similar backgrounds including an alcoholic mother and being shunted between different care givers as children. One did poorly and one did very well. Capote described it as if both of them grew up in the same house with the murderer going out the back door and Capote going out the front.
Wednesday, November 16, 2005
The Anthropic Cosmological Principal
Why have things worked out so well for us. It seems that the universe was designed for the existence of human beings? Many of the fundamental forces and constants of nature are such the we can exist. Even relatively small changes in these values would result in a universe that is not compatible with our biological existence. IF gravity were just a little stronger there would be nothing but black holes. If it were weaker stars and planets would not form. If the mass of the electron was different chemical reactions would not be possible.
The weak anthropic principle says that the reason things look so good is that if they were different we wouldn’t be here to ask the question. So there is self selection in that other universes with other values for critical forces and masses wouldn’t support us. The strong anthropic principle says the somehow something designed the universe to be just right for us. The book “The Anthropic Cosmological Principle” by John D. Barrow, Frank J. Tipler uses almost 700 pages to go into the alternatives in great depth. It describes each of the forces and critical constants in great detail to firmly establish uniqueness of our situation. It does this with multiple differential equations and level three tensors so a little mathematical expertise helps in understanding the arguments. I recommend this book to anyone with a lot of interest and a lot of time.
Monday, November 14, 2005
The Search for Adam
Well, there is even more proof that we are a very young species. Today I viewed an impressive documentary on the National Geographic Channel describing work by Spencer Wells on the relatedness of all men. He used DNA sequences from the human Y chromosome. This chromosome was chosen because it doesn’t have a mate. Men are XY and there are no common sequences between them. Other chromosomes including the X in women have a mate or sister chromatid with which recombination can happen during the development of eggs or sperm. Recombination or exchanges between of parts of one chromosome with its mate scrambles the genetic pattern after a few generations. Since the Y has no mate it can’t undergo recombination so it’s sequence does not change except for mutation. Wells follows the rare mutations on the human Y chromosome to get a pattern of relatedness. This analysis shows all human Y chromosomes trace back to a single line that existed about 50,000 years ago. The number of mutations detected act as a somewhat imperfect clock. Mitochondrial DNA which is only inherited through women provides a similar means of analysis that traces the female line. Mitochondrial DNA has previously been used to trace our lineage back to a single women or small group of individuals. Thus both independent types of analysis come up with approximately the same answer although the mitochondrial eve seems to be somewhat older than the Y man. Both analyses say the we are a very young species that took over the world in a relatively short period of time. The author notes that the usual depictions of Adam as a light skinned European is incorrect. He was African.
I highly recommend this program. Information can be found at the link below.
http://www.nationalgeographic.com/adventure/0508/excerpt1.html?fs=www5.nationalgeographic.com
Saturday, November 12, 2005
Fox Hunting in Hollis NH
Today was a beautiful day with the members of Hunt dressed in their “pinks” chasing after the hounds. This area provides wide open fields where the work of the hounds can be viewed at a distance adding an extra dimension to the sport for hunters and spectators alike. Only one person was unseated and had to remount. This was much better than last week at a differnt hunt were a participant had to helicopterd off the field to a hospital because of a fractured pelvis. Orthopedic surgeons make a lot of money off this sport. After the hunt members enjoyed recounting their exploits at an excellent tea hosted by a local land owner.
Friday, November 11, 2005
Onset MA, Intelligent design and dating with DNA sequences
Today I had a great trip to see an old friend and his new house on Onset beach. They have an excellent view with the beach just across the road. He showed me all the modifications they had made and are making to modernize the house. It is quite nice. We drove to Woods Hole on Cape Cod for lunch with additional excellent water views including some of the oceanographic vessels.
Yesterday I talked about the great amount of proof that exists for the theory of evolution including geologic and isotopic dating. This evidence has been available for some time. The newer evidence comes from the genetic code itself. As gene sequencing has advanced an incredible amount of data has become available. There is so much that it is difficult to find computer systems large enough to store and analyze it. The combination of sequence data from a growing number of organisms with extreme computing power has allowed one to do genetic analysis predominately on the computer. NIH sponsors GenBank http://www.ncbi.nlm.nih.gov/Genbank/ which is one of the largest databases available. If you know a sequence this will tell you which other organisms contain that same sequence. The database currently exceeds 100 gigabases. Once the sequences have been established there is no more need for test tubes. This resource makes it possible to determine the relationships between organisms exclusively on the computer and you can do it from home!
The number of differences between two species is relatively proportional to the time in the distant past in which their common ancestor existed. This estimate of time can be compared to those from geology and isotopic dating. In general, they all agree. The answer is a long time ago. Dating techniques that are so different chemically that give the same answer are very difficult to refute. How could they all be wrong? The only alternative explanation is that the intelligent designer made the world in 4004 BC but did it in such a way as to make it look very old. It is an interesting theory but one for which there is no scientific evidence. By the way, an example of intelligent design is provided in the recent movie “The Hitchers Guide to the Universe”. All current evidence says that the world is very old and that evolution took a long time making one small change at a time. The changes were subjected to natural selection with those that were beneficial at that time and in that environment carrying on to the next generation. There is no need for intelligent design.
Another argument is that our biology is extremely complex. Any intelligent designer would not have been so messy. Groups are now attempting to make a simple organism from scratch. I am sure that it will be much less messy than those organisms that evolved the natural way.
One more thought, by examining the sequences of related genes, i.e. those that produce products that have a similar function one can see how one was derived from another. Often we see that a gene is duplicated on a chromosome and that the two copies start to evolve separately. One can examine the sequences and see how they diverged, one mutation at a time eventually taking on different functions in the cell’s metabolism. Sometimes on sees sequence changes that make no functional difference. Why would an intelligent designer bother with changes that make no difference?
One can never exclude intelligent design but it isn’t needed to explain how we got here.
Thursday, November 10, 2005
A suggestion for the intelligent design folks
The teaching of intelligent design is a hot subject. There is a fight between the secular scientists pushing evolution and religious groups advocating intelligent design. The intelligent design folks are going after the wrong group. They have a much better case against the cosmologists than the geneticists. The theory of evolution can do one thing that intelligent design can’t and that is predict things. If you want to breed plants or animals, design new pharmaceuticals, understand the relatedness of organism, the modern theory of evolution and genetics can predict outcomes of experiments and breeding programs. Intelligent design provides no such guidance. It can’t predict anything. The whole purpose of a theory is to be able to predict things or it is worthless. One might accept it on the basis of religious belief but it has no use in the physical world we live in. When Darwin and others created the theory of evolution they had very little proof other than the pattern of plants and animals seen on the earth at that time. Geology was suggesting an ancient earth but there was little corroborating evidence. Today there are many independent disciplines that support the original theory in general. The theory of radioactive decay fits very well with the predictions of an ancient earth. Looking at the abundance of decay products is an excellent estimator of the age of a chemical system. These age determining techniques depend on the same theories that allow the design of atomic bombs and medical radiation therapy. If one challenges the dating then one has to deny the existence of nuclear fission and fusion. This shows one level of conformation by an independent discipline. Modern molecular genetics using DNA sequencing and sequence comparisons also support the dating provided by the theory of evolution. I will talk more about this tomorrow.
The area of science that is weak is cosmology or the study of the origin of the universe. Intelligent design is really a cosmology or a way to explain how we got here. The most advanced cosmologists have the same problem as the intelligent design groups in that they can’t predict anything. The energies required to look at the strings they hypothesize as being at the route of all matter are too small to be “seen” by any conceivable atom smasher. So the intelligent design folks should go after the cosmologists and leave us geneticists alone.
Wednesday, November 09, 2005
Mapping Groton MA
http://www.geozone.com/Groton/
Tuesday, November 08, 2005
Foxing in Lexington
Monday, November 07, 2005
Hum’s Birthday and Dingy Retrieval
Happy birthday congratulations to Hum, Master of Fox Hounds and all around good guy.
Today Tiny and I drove up to South Freeport in my wife’s truck to bring my dingy home. I pulled it out of the water a couple of weeks ago to let the gunk on the bottom dry out. Today we pulled it up a ramp from the dock and put it in the back of the truck. It was tied in very well. My outboard had been winterized and could be brought it home as well. The day was mild but very windy. It was a coincidence that my Ericson 35 was still in the water. The staff at Brewers had winterized the systems. As we were about to leave Kristin was bringing it around from the dock to the rigging pit to have the mast removed for the winter. It will then be lifted out of the water and put on stanchions for the winter. Before too long they will shrink wrap it although the price of shrink wrap has gone up dramatically as the same plastic is used for siding that is in high demand due to recovery from the hurricanes. Hopefully my craft will be soon ready to sleep through the winter.
Sunday, November 06, 2005
How do we get so many types of antibodies to fight disease?
At one time many thought that our immune cells would encounter an invader and then make unique antibodies that would destroy the invader. This turned out not to be the case. We know of no molecular mechanism that could create such molecules de novo. However, it turned out that we from our genes we make millions of different immune cells each making one type of antibody. The ones that react with our tissues are killed off at an early stage. The fraction of the cells that don’t react with us are continually testing chemicals in their environment to see if there is something there that they can bind with. Usually these chemicals are pieces of bacteria or viruses that are trying to invade us. If binding occurs then this clone of cells expands dramatically so that there are enough of them to fight off the invader. Some cells make antibodies that float around in the blood and another type of cells attack the invader directly. So we don’t encounter a chemical and then create an antibody that will bind to it but amplify a clone of cells that already have such a reactive antibody on their surface. The antibodies come from our genes and are not made de novo in response to a specific chemical.
The whole process is much more complicated that my simplistic description but basically that is how it works..
Friday, November 04, 2005
Recovery from knee surgery for the removal of a torn meniscus
Today the excellent doctor that took out my torn meniscus took out the stitches from the arthroscopic surgery he did about a week and a half ago in Nashoba hospital. Things are going well but the knee aches at night, especially if I have been hiking with my dog. Dr. H was nice enough to give me some pictures taken during the operation. The red stuff is arthritic inflimation if I understood him correctly. He scraped some of it out as long as he was in there. The torn meniscus can be seen in the third picture down on the right as a roll of tissue before its removal. The process has been very interesting except that I could have done without the pain and incapacitation.
Wednesday, November 02, 2005
The classification of all life
I have been interested in RNA life for some time. It is the only way to avoid the chicken or egg problem. What is needed is a single molecule that can carry the genetic code and also catalyze chemical reactions. However, there are some problems as listed below. The panspermia people say that life came from outer space and seeded a young earth. That may be so but then how did that life originate?
From www.panspermia.org/rnaworld.htm
The RNA World What'sNEW
Virtually all biologists now agree that bacterial cells cannot form from nonliving chemicals in one step. If life arises from nonliving chemicals, there must be intermediate forms, "precellular life." Of the various theories of precellular life, the most popular contender today is "the RNA world."
RNA has the ability to act as both genes and enzymes. This property could offer a way around the "chicken-and-egg" problem. (Genes require enzymes; enzymes require genes.) Furthermore, RNA can be transcribed into DNA, in reverse of the normal process of transcription. These facts are reasons to consider that the RNA world could be the original pathway to cells. James Watson enthusiastically praises Sir Francis Crick for having suggested this possibility (1):
The time had come to ask how the DNA—>RNA—>protein flow of information had ever got started. Here, Francis was again far ahead of his time. In 1968 he argued that RNA must have been the first genetic molecule, further suggesting that RNA, besides acting as a template, might also act as an enzyme and, in so doing, catalyze its own self-replication.
It was prescient of Crick to guess that RNA could act as an enzyme, because that was not known for sure until it was proven in the 1980s by Nobel Prize-winning researcher Thomas R. Cech (2) and others. The discovery of RNA enzymes launched a round of new theorizing that is still under way. The term "RNA world" was first used in a 1986 article by Harvard molecular biologist Walter Gilbert (3):
The first stage of evolution proceeds, then, by RNA molecules performing the catalytic activities necessary to assemble themselves from a nucleotide soup. The RNA molecules evolve in self-replicating patterns, using recombination and mutation to explore new niches. ... they then develop an entire range of enzymic activities. At the next stage, RNA molecules began to synthesize proteins, first by developing RNA adaptor molecules that can bind activated amino acids and then by arranging them according to an RNA template using other RNA molecules such as the RNA core of the ribosome. This process would make the first proteins, which would simply be better enzymes than their RNA counterparts. ... These protein enzymes are ... built up of mini-elements of structure.
Finally, DNA appeared on the scene, the ultimate holder of information copied from the genetic RNA molecules by reverse transcription. ... RNA is then relegated to the intermediate role it has today—no longer the center of the stage, displaced by DNA and the more effective protein enzymes.
Cech
Today, research in the RNA world is a medium-sized industry. Scientists in this field are able to demonstrate that random sequences of RNA sometimes exhibit useful properties. For example, in 1995, a group of researchers reported "Structurally Complex and Highly Active RNA Ligases Derived from Random RNA Sequences" (4). (Ligases are enzymes that splice together other molecules such as DNA or RNA.) The results are interesting—they suggest that randomness can produce functionality. The authors interpret the results to mean that "the number of distinct complex functional RNA structures is very large indeed." There is a lot to learn about RNA, and research like this is how we learn it. But these and other similar findings arrived at in highly orchestrated experiments that start with biologically produced RNA are very far from proving that the RNA world is the pathway between nonlife and life. In nature, far from the sterilized laboratory, uncontaminated RNA strands of any size would be unlikely to form in the first place. "... The direct synthesis of ... nucleotides from prebiotic precursors in reasonable yield and unaccompanied by larger amounts of unrelated molecules could not be achieved by presently known chemical reactions" (5).
Crick
Francis Crick himself has become much less enthusiastic about the RNA world than Watson. In 1973, he and another eminent researcher into the origin of life, Leslie E. Orgel, published a paper advocating the theory of "Directed Panspermia" (6). In 1981, Crick published Life Itself, a whole book about that theory (7). And by 1993 he says, "It may turn out that we will eventually be able to see how this RNA world got started. At present, the gap from the primal 'soup' to the first RNA system capable of natural selection looks forbiddingly wide" (8).
At the Salk Institute for Biological Studies, in 1994, Leslie Orgel observes, "Because synthesizing nucleotides and achieving replication of RNA under plausible prebiotic conditions have proved so challenging, chemists are increasingly considering the possibility that RNA was not the first self replicating molecule..." (9).
Apparently NASA has lost enthusiasm for the RNA world as well. In the Final Report issued after the "Astrobiology Workshop" held September 9-11, 1996 at Ames Research Center, California, we read (10),
It has been postulated that there was a time in protobiological evolution when RNA played a dual role as both genetic material and a catalytic molecule ("the RNA world"). However, this appealing concept encounters significant difficulties. RNA is chemically fragile and difficult to synthesize abiotically. The known range of its catalytic activities is rather narrow, and the origin of an RNA synthetic apparatus is unclear.
Other Theories
In spite of the intense level of work on the RNA world in the last decade, there is no consensus theory for precellular life. There are many theories. Here are some of the others —
A few scientists still say that DNA could succeed in starting life on its way (11). But even the shortest DNA strand needs proteins to help it replicate. This is the chicken-and-egg problem.
There is a "proteins first" school. For example, Manfred Eigen of Germany's Max Planck Institute says, "There is no doubt that proteins, which are more easily formed, were first on the scene" (11.5). Of course, these first proteins must be much shorter than any used in life today, because of the sheer unlikelihood of forming useful long ones out of a soup of amino acids.
Physicist Freeman Dyson proposes to solve the chicken-and-egg problem with a double origin, one for metabolism (proteins) and one for replication (strands of nucleotides) (12).
In Seven Clues to the Origin of Life (13), A. G. Cairns-Smith says that clay crystals could have served as the scaffolding upon which the first short DNA or RNA genome was constructed. A new elaboration of this idea prompted one writer to wonder, "Primordial soup or crêpes?" (14). Even more recently, another tangent on this path leads to zeolite (14.5).
Biologists Harold J. Morowitz (15), David Deamer (16), and others (17), advocate a theory that could be paraphrased as "containers first."
Jeffrey L. Bada of the Scripps Institution of Oceanography holds the minority view that the early Earth was frozen and believes precellular life started in "cold soup" under the ice (18, 19).
Chemists Claudia Huber and Günter Wächtershäuser say the soup where life originated was actually quite hot, probably, near undersea volcanic vents, where iron and nickel sulfides might catalyze some of the necessary reactions (19.5-19.7).
Cornell Astronomer Thomas Gold wonders if life might have originated in a hot environment even deeper, in Earth's crust (19.8).
Stuart Kauffman of the Santa Fe Institute, says, "...whenever a collection of molecules contains enough different kinds of molecules, a metabolism will crystallize from the broth" (20).
Another idea is the "PNA world." Because starting the RNA world is so difficult, there probably needs to be a pre-RNA world. PNA, or peptide nucleic acid, might have some of the properties necessary to constitute that world (21). This would be pre-precellular life.
The Time Problem
To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. — Lynn Margulis (21.5)
The only premise that all of the precellular theories share is that it would be an extremely long time before the first bacterial cells evolved. If precellular life somehow got going, it could then conceivably begin to crank out, by some precellular process, random strings of nucleotides and amino acids, trying to luck into a gene or a protein with advantages which would lead to bacterial life. There is no evidence in life today of anything that produces huge quantities of new, random strings of nucleotides or amino acids, some of which are advantageous. But if precellular life did that, it would need lots of time to create any useful genes or proteins. How long would it need? After making some helpful assumptions we can get the ratio of actual, useful proteins to all possible random proteins up to something like one in 10^500 (ten to the 500th power). So it would take, barring incredible luck, something like 10^500 trials to probably find one. Imagine that every cubic quarter-inch of ocean in the world contains ten billion precellular ribosomes. Imagine that each ribosome produces proteins at ten trials per minute (about the speed that a working ribosome in a bacterial cell manufactures proteins). Even then, it would take about 10^450 years to probably make one useful protein. But Earth was formed only about 4.6 x 10^9 years ago. The amount of time available for this hypothetical protein creation process was maybe a hundred million or 10^8 years. And now, to make a cell, we need not just one protein, but a minimum of several hundred.
So even if we allow precellular life, there is a problem getting from there to proteins, genes and cells. The random production of proteins does not succeed as an explanation. Other intermediate, unspecified stages must be imagined. We could call these stages post-precellular life. By whatever means, life's evolution through these stages would have to be time-consuming.
One advocate of the RNA world, Gerald Joyce, allows 400 million years for "The Rise and Fall of the RNA World" (22):
...At some point RNA organisms began to dabble in the use of short peptides, leading eventually to the development of protein synthesis. Other "experiments" led to the discovery of DNA, which provided a more stable repository for genetic information. By 3.6 to 3.8 billion years ago all of these events had come to pass; the RNA world had fallen and the DNA/protein world had risen in its place.
But other researchers see evidence for prokaryotic cells in the first 100 million years, maybe even immediately. "...Actual cells have been found in the earth's oldest unmetamorphosed sediments...," says Gould in Wonderful Life (23). Bada says that cyanobacteria may have emerged only ten million or 10^7 years after the first precellular life (24). In November, 1996, S. J. Mojzsis of the Scripps institution of Oceanography and others reported isotopic evidence that cellular metabolism was under way before 3.8 billion years ago (25). Even before the research by Mojzsis et al., Francis Crick was worried by the time problem. "...The real fossil record suggests that our present form of protein based life was already in existence 3.6 billion years ago.... This leaves an astonishingly short time to get life started" (26). Another researcher, Peter B. Moore, says this about the time problem (27):
Of one thing we can be certain: The RNA world—if it ever existed—was short-lived. The earth came into existence about 4.5 x 10^9 years ago, and fossil evidence suggests that cellular organisms resembling modern bacteria existed by 3.6 x 10^9 years before the present.... There are even hints that those early organisms engaged in photosynthesis, which is likely to have been a protein-dependent process then, as now. Thus it appears likely that organisms with sophisticated, protein based metabolisms existed only 0.9 x 10^9 years after the planet's birth.
The "window of opportunity" for the RNA world was much shorter than 0.9 x 10^9 years. The earth's surface was uninhabitable at the beginning due to heat generated by meteoric bombardment and its geological differentiation. ...Thus, the interval in which the biosphere could have been dominated by RNA-based life forms may be less than 100 million years. Incidentally, when one starts thinking along these lines, one must consider the unthinkable, i.e., that the length of time that RNA-based proteins actually bestrode the earth might be zero.
Tuesday, November 01, 2005
MRI and Soylent Green
This whole process reminded me of the science fiction movie Soylent Green. This movie was set in the future at which time the world was severely over populated. One of their tactics was to talk people into ending it all at termination centers. The subject would go in and in a pleasant environment they would kill you by chemical injection. You were allowed to choose music and I believe the lighting color or picture you wanted as you passed over. Then your body would be boiled down and made into food bars called Soylent Green. The sanitary environment and choice of music at the MRI center reminded me of this movie. Fortunately I am still here and am not a breakfast bar.
Monday, October 31, 2005
Knee developments
Saturday, October 29, 2005
Fox hunt in Stow and knee surgery recovery and oxycontin or oxycodone
The Old North Bridge Hounds held a mock fox hunt in Stow MA at the Delaney park. The day was beautiful and the field was impressive with the women in their black coats with the senior men in their red or “pink” coats. An excellent tea was held at a new member’s house across the street from the park. Because of my knee I was not able to help with laying the drag but arrived in time to congratulate the “Foxes” good efforts. While my knee has improved significantly it is not done yet. There is a continual ache that I treat with ibuprofen or Tylenol avoiding the opiates that worked so well. A friend suggested that oxycontin and oxycodone were different drugs. They are really the same thing. As noted below, drug abusers often take the drug by snorting the powder or injecting an extract to expand the effect. In my past life in drug testing it provided difficulties as it is stronger on a weight basis than heroin and therefore less is used to get high. As less is used there is less in the body and detecting it is more difficult. It is addictive and produces tolerance so should be used only for a short time and with care. I moved to other pain relievers as soon as I could to avoid the problems of tolerance and addiction. For me ibuprofen seems to work better than acetaminophen.
From www.streetdrugs.org
Oxycodone (OxyContin, Percocet, Percodan)
Oxycodone is a central nervous system depressant. Oxycodone's action appears to work through stimulating the opioid receptors found in the central nervous system that activate responses ranging from analgesia to respiratory depression to euphoria. People who take the drug repeatedly can develop a tolerance or resistance to the drug's effects. Thus, a cancer patient can take a dose of oxycodone on a regular basis that would be fatal in a person never exposed to oxycodone or another opioid. Most individuals who abuse oxycodone seek to gain the euphoric effects, mitigate pain, and avoid withdrawal symptoms associated with oxycodone or heroin abstinence.Oxycodone has a high abuse potential and is prescribed for moderate to high pain relief associated with injuries, bursitis, dislocation, fractures, neuralgia, arthritis, and lower back and cancer pain. It is also used postoperatively and for pain relief after childbirth. OxyContin, Percocet, Percodan, and Tylox are trade name oxycodone products.OxyContin is designed to be swallowed whole; however, abusers ingest the drug in a variety of ways. OxyContin abusers often chew the tablets or crush the tablets and snort the powder. Because oxycodone is water soluble, crushed tablets can be dissolved in water and the solution injected. The latter two methods lead to the rapid release and absorption of oxycodone.
Friday, October 28, 2005
Less weight more brain
A genetically engineered mutein of CNTF being tested under the name Axokine by Regeneron Pharmaceuticals for treatment of human motor neuron diseases.
Unfortunately people taking Axokine developed antibodies against the drug and the effects were short lived. However, Flier’s studies in mice showed that the drug stimulated neuronal growth in the brain’s hypothalamus know as a regulatory center. More neurons were created that responded to the natural appetite suppressor Leptin thus reducing hunger .
This drug is not a small molecule but a genetically engineered protein and therefore more likely to elicit an immune response than a small molecule. It is interesting that Regeneron is working on a PEGilated version of this protein. This process involves attaching molecules of the short polymer polyethylene glycol to the surface of the protein. The idea is that the PEG molecules keep the immune system from recognizing and attacking the protein so protected. Perhaps there is more to come.
Thursday, October 27, 2005
Embryonic stem cells without killing babies
Tuesday, October 25, 2005
Recovery from surgery
Monday, October 24, 2005
Arthroscopic surgery complete at Nashoba Valley Hospital
Today the broken cartilage was removed from my injured knee. I was impressed by the friendliness and professionalism of the staff and surgeon. My wife gave great support. I have kept the medications as low as possible and was not in extreme pain. When I was in high school many years ago I broke the meniscus in my left leg. This was before arthroscopic surgery and was more involved as I was in the hospital a couple of days. They did a spinal that gave me severe headaches. This time there were no problems and I was out of the hospital by late afternoon. Medicine advances.
Saturday, October 22, 2005
Fox Hunt with a Wedding
Today was the blessing of the hounds for the Old North Bridge Fox Hunt. This solemn event was combined with the marriage of a hunt member to another hunter from Tennessee. Everything went off beautifully with the marriage ceremony in a green pasture under an arch of flowers. The hunt members attended the wedding on their horses in full dress with “pink” coats and green collars giving three cheers after the bride was kissed. The minister then moved to the waiting hounds and with the newly married couple blessed the hounds. With the festivities completed the riders took off after the hounds through the trails of Concord. I wasn’t able to help lay the drag because of a knee problem but watched with the chief fox who laid the drag as the hounds followed the scent through a field. They did a rather good job of following the scent through the grass. An excellent tea took place after the hunt with abundant champagne. Near the end of the tea my wife called me over to meet someone. It turned out to be the daughter of the master of her first hunt which she joined when we lived in New Jersey. We hadn’t seen Meg in years. It was a real treat.
Friday, October 21, 2005
Macular Degeneration and siRNA
Macular degeneration is the leading cause of severe vision loss in people 60 years of age or older in the United States and throughout many parts of the world.
The treatment for macular degeneration listed below is a major accomplishment for two reasons. First, it is a treatment for a disease that is becoming more prevalent as the population ages. Second, the therapy uses the new siRNA technology. This treatment uses a short strand of RNA in a special configuration that turns off a vascularization gene by binding with its RNA. It is the sequence of the siRNA that makes it specific for the endothelial growth factor (VEGF) gene and causes the proteins manufacture to be turned off. The technique is very general so can be applied to almost any gene. I believe that siRNA will bring about a revolution in medicine.
Phase II Trial Starts for siRNA Therapy for Wet AMD
10/19/2005
Acuity Pharmaceuticals initiated a Phase II trial for Cand5, its lead product candidate for the treatment of wet age-related macular degeneration (wet AMD), following successful completion of Phase I trial.
According to the company, this is the first-ever Phase II program for a small interfering RNA (siRNA) therapy, based on the gene silencing technology of RNA interference (RNAi).
Acuity, founded in 2002, has an exclusive license to several types of RNAi intellectual property from the University of Pennsylvania, including both broad-based and target-focused applications.
“Cand5 is safe and well-tolerated in patients with wet AMD,” said Jonathan L. Prenner M.D., of UMDNJ—Robert Wood Johnson Medical School and an investigator for Acuity’s Phase I study.
Cand5’s RNAi mechanism silences the genes that promote the overgrowth of blood vessels that lead to vision loss in wet AMD by shutting down the production of vascular endothelial growth factor (VEGF), which has been shown to be the central stimulus in the development of wet AMD.
By stopping production of VEGF at the source, Cand5 is expected to have efficacy advantages over other types of therapies for wet AMD, which work by inhibiting VEGF only after it has already been produced in the the eye, explained Dale Pfost, Ph.D., president and CEO of Acuity.
“A single molecule of Cand5 repeatedly stops hundreds of VEGF molecules. This sustained duration of action could result in less frequent delivery, perhaps only four to five times per year,” asserted Dr. Pfost.
Acuity’s Phase I trial, an open label, dose-escalation study that included 15 patients, tested five dose levels administered by intravitreal injection at six-week intervals. Cand5 was shown to be safe and well tolerated following repeat administration of the escalating dose levels, up to 3.0 mg per eye.
This study also included a pharmacokinetic analysis indicating that the study drug was not present in the plasma of any of the patients at any of the doses tested. This absence of systemic exposure to Cand5 is signficant since powerful VEGF inhibitors have the potential to cause serious adverse effects if present systemically, notes Dr. Pfost.
Wet Age-Related Macular Degeneration
Wet Macular Degeneration occurs when abnormal blood vessels start to grow on the center of your retina. These new blood vessels may be very fragile and often leak blood and fluid. The blood and fluid can damage your macula or create a scar on your retina, causing vision problems. Damage to the macula can occur rapidly, causing a noticeable loss of central vision. The vision loss from wet macular degeneration may be permanent, because abnormal blood vessels and scar tissue are actually replacing normal retina tissue. Once lost, these light-sensitive cells in your retina cannot be replaced.
An early symptom of wet macular degeneration is vision change, when straight lines appear wavy. For example, you may notice that your door frames appear wavy instead of straight. If you notice this condition or other changes in your vision, contact your eye care professional immediately for a comprehensive dilated eye exam. Treatments are available that may slow and reduce vision loss associated with wet macular degeneration. You should report any changes in vision to an eye care professional as soon as you notice them.
It is estimated that more than 2 million people in the United States currently have wet macular degeneration, with an increase of 200,000 new cases