A place I can put my thoughts on science, teaching and the human condition, and also occasionally attempt to influence policy makers (lots of luck!).
Wednesday, December 2, 2009
Finally action
Today there was a article in the LA Times stating that the DWP Commissioners approved a 600 acre pilot project to do just that. It made my heart beat a little faster.
Friday, November 20, 2009
A Crisis in Public Education
The students might be interested in a small fruitless battle I led recently attempting to convince the UCLA administration not to misallocate the scarce resources of the State. I copy the letter I sent to the UCLA Chancellor below:
“I am a Professor in the Department of Microbiology, Immunology and Molecular Genetics and have been at UCLA for the last 41 years. I find it hard to believe that UCLA is going forward with a $185 million renovation of Pauley Pavillon at a time when courses are being eliminated and faculty and staff salaries are being cut. The article in UCLA Today states that, out of the required $185 million, "..we have $52 million that has been committed to date toward that goal..", and that the remainder of the funding will come from "..$15 million in Student Programs, Activities and Resources Center fees and $10 million in Student Seismic fees.." and "..$60 million in external financing..". The article attempts to justify this expenditure by stating that ".. this is an important symbol of UCLA's overall reputation for excellence.." However, the symbol of excellence for a great University is the quality of its faculty in teaching and research, not athletics and public events and concerts. … This is a true misallocation of scarce resources at this time of financial crisis and should be reversed.”
About the same time, there was a Letter to the Editor of the LA Times by the ex Chair of the committee involved in the Pauley renovation project, who was fired when he complained about the proposed huge increase in costs. This letter provided additional factual information which made my letter seem a drop in the bucket.
I received in due course a response from the "Vice Chancellor for External Affairs" which attempted to justify these planned expenditures but succeeded only in strengthening my objections. At that point I saw the futility of it all and let it ride. But now it would appear that this misallocation of scare resources has come home to roost.
Sunday, October 18, 2009
Shedding Light on Solar
To do my little part, I have finally decided to get solar panels installed on the roof of our house. The electricity generated will be sent into the grid and the electric company will deduct this from our bill. And therein lies the rub! Any electricity generated by my solar panels over and above what we use in the house is gladly taken by the electric company with no recompensation or even a thank you. This, I feel is one of the major non-technological stumbling blocks to universal decentralized solar power. Beyond the normal and customary bureaucratic madness, I can only surmise that the electric company wants to maintain a monopoly on the generation of electric power and feels threatened by this new zeitgeist. It is a no-brainer that paying residents for residential energy production will greatly stimulate its adaption and utilization. Of course, there remains the problem of energy transmission and temporal variability of production when it depends on the sun shining through the clouds. I have read that so-called "smart grids" could be able to solve these problems, but that is another story.
The astute reader of my blog will notice that I have not mentioned nuclear energy. True, nuclear energy does not produce greenhouse gases, but it produces something even worse, the high level radioactive waste that cannot be safely stored anywhere for the requisite tens and even hundreds of thousands of years into the future. Remember, human civilization only began several thousand years ago when hunter-gatherers formed cities and began growing their food and domesticating animals, and the industrial age only began in the 19th century! No, I did not mention nuclear energy since I feel it is a problem and not a solution.
Tuesday, August 18, 2009
Some musings on health Care
One often but not always learns best by comparisons with others. For example, in every other civilized industrialized country in this world, health care is a right, not a privilege, and is provided by the government to everyone in that country, even to visitors. By this reasoning, I came to the conclusion years ago (especially in the last 8 years) that our country must not be civilized, at least from this point of view. But then Obama was elected and I saw some hope on the horizon. I must admit that he has not been perfect. He appears to have been swayed too much by the intelligence agencies and military in such policies as continuing warrantless wiretapping of American citizens, in not prosecuting people at the top who broke the law in the previous administration, in not releasing the latest torture photos, in not pushing for gun control, in not yet completely leaving Iraq, and more recently, in not pushing for Medicare for everyone as the solution to health care reform. But in most other areas, he has been great and has returned our country to the status of an almost civilized country.
The Health Care controversy has once again made me have some doubt about the level of civilization in our country. Why on earth would anyone be against providing health care for everyone and stopping the predatory practices of the health insurance companies who now rule our medical lives? It can not be the shouted out argument that government should not run health care or even pay for it, since the popular Medicare program is government run and is very efficient and successful. Even those opposing health care reforms would not give up Medicare and also would not return those checks from Social Security they receive each month when they turn 65. So why is this occurring? The only reason I can think of is that this reform would hurt the profits of the giant health care insurance companies so they are paying huge sums of money to prevent this. This money is spent both in advertising to sway public opinion and in "campaign contributions" to the very members of Congress and the Senate who will have to vote on this type of bill. To connect the company money with opposition to reform implies that these politicians will be swayed (i.e. bribed) by the contributions to vote however the companies desire, but this unfortunately appears to be the case. There can be no other reason. And the politicians do not have to worry about health care since they are covered by a government financed program and will be covered their whole lives (I believe).
Monday, August 3, 2009
The lights in the sky are stars
Any time I feel cocky and start thinking what a great teacher and scientist I am, I look up to the stars and realize that we and the entire earth we live on are simply a tiny, tiny, tiny blip in the Universe. The light actually left the stars years or even thousands of years ago and just now arrived here. And the panorama of stars one sees (if one is lucky enough not to live in Los Angeles) does not really exist, but represents slices of history, with each star releasing its light at different times in the past, with some probably not even existing anymore. And the light from the billions of stars in the billions of galaxies was emitted millions to billions of years ago and has endured the most incredible trip one could imagine to get to us here on earth. Sometimes this is too just much to comprehend, so I start out by trying to visualize distances. I start with the understandable - the distance from here to the other side of my yard, then from my city to another city and from my country to another country. I understand this because I have walked across the yard and have stared out the small window of an airplane flying several miles above the earth for 10 hours. Looking at my flight from here to London on a globe gives me a feeling for the size of the earth. To get to the moon, it would take my jet plane around 16 days since it is around 30 earth-diameters distant; it even took the Apollo astronauts 3-4 days with a much bigger jet plane. I can see the moon and can easily grasp this distance with some stretching of the imagination and can even imagine that I see the lunar lander left behind when the astronauts departed. But then things get a little hairy. Light from the nearest non-sun star, Proxima Centauri, which I can easily see with my 10 inch telescope, took 4.2 years to reach me, and light travels really fast - around 670 million miles per hour. Now I am struggling with the concept, but worse is yet to come. Light from our closest neighboring galaxy, Andromeda, took 2.5 million light years to arrive here, and light from the farthest object yet observed, a stellar explosion that released an immense amount of gamma-rays, took 13 billion years to arrive here. Now it is just numbers, but numbers do have meaning and the meaning is that I myself am meaningless in the immensity of it all and am properly chastened.
Wednesday, July 22, 2009
A modest proposal
And in the near future another such site will unfortunately become available by the inevitable drying of the Salton Sea.
Postscript added on Aug. 17.
I don't want to brag but I just read a news article about covering the Owens dry lake with solar collectors (http://abclocal.go.com/kabc/story?section=news/state&id=6966498). In addition to the above Blog posting, I had written the Department of Energy and also a solar company that plans to open a large solar plant in the Mojave desert (with no responses of course). In any case, I am sure that this idea was so obvious that it occurred to many people previously.
Science is a hard mistress
I myself have experienced both types of emotions in my research career. The high came in 1990 when we suddenly realized that we could explain the extremely enigmatic and even disturbing phenomenon of uridine insertion/deletion RNA editing in trypanosomes that was causing serious scientists to speculate that the genetic dogma of information flow from DNA to RNA to protein was incomplete. We and others had found that multiple transcripts of the maxicircle mitochondrial DNA in trypanosome mitochondria could not be translated due to the absence of open reading frames, and that these transcripts were somehow corrected after transcription by the insertion and occasional deletion of uridine residues at specific sites thereby eliminating the encoded frame shifts and producing mRNAs with open reading frames that encoded conserved mitochondrial proteins. Initially the phenomenon was thought to involve a few U’s at a few sites, but soon it blossomed into cases of hundreds of U’s at hundreds of sites, in essence creating genes de novo.
The overriding question was where did the information come from that told the U’s to be inserted and deleted at these precise sites. The information did not appear to be encoded anywhere in the mitochondrial genome, which was in itself quite bizarre in that it consisted of around 50 maxicircles catenated with thousands of minicircles into a single giant network of DNA. Not giving up on the central dogma we were looking for RNAs that could base pair with mature edited sequences and thereby provide the information by this well tested mechanism. We speculated that perhaps the reason no one had seen this sequence information was that it was in short segments. Having asked our friendly lab computer to search for short sequences anywhere in the maxicircle genome that could base pair with the mature edited sequences and thereby encode the insertions and deletions of U’s, it was at first disappointing that there were no such antisense sequences. But a closer examination of the results showed that the mismatches were always transitions and suddenly we realized that if we took off our Watson Crick blindfolds and simply allowed G-U base pairs in addition to G-C and A-U base pairs, the computer was telling us that there were short complementary sequences in the maxicircle DNA that could encode the editing information. A few days later we obtained some direct evidence for the existence of a novel class of small RNAs with these sequences (and also with 3’ non-encoded oligo U tails!) and we named them “guide RNAs”.
The next high came when we (i.e Nancy Sturm, my graduate student) realized that the thousands of minicircles also actually encoded the majority of guide RNAs and that this was finally the long sought after solution to the genetic function of minicircles. Suddenly we had two mitochondrial genomes in the same cell, one with cryptogenes and another one with complementary guide RNA genes. Immediately this discovery led to a mechanism in which the gRNAs formed an anchor duplex with the pre-edited mRNA just downstream of the editing site and recruited a cadre of specific enzymes to the editing site. We proposed a nuclease that cleaved the pre-edited mRNA at the editing site, a 3’ terminal uridylyltransferase that added U’s or an 3’-5’ U-specific exonuclease that deleted U’s, and finally an RNA ligase that religated the cleavage fragments. Like all good models it was very satisfying since it explained a number of previous observations such as the 3’ – 5’ polarity of editing. This was a definite high in the life of my lab.
But my Swiss postdoc, Beat Blum, had the habit of thinking too much and soon came up with another model - in which the U’s were transferred from the known 3’ oligo U tail of the gRNAs to the editing sites by a transesterification mechanism such as employed in RNA splicing. This model had an easily testable prediction – that there were chimeric intermediates in which the 3’ end of the gRNA was covalently linked to the mRNA 3’ cleavage fragment at an editing site. When this was rapidly confirmed, the lab entered another high, albeit with a low level of anxiety and chagrin that we had just proposed another seemingly viable model and now were saying that this was wrong. The transesterification model became the flavor of the week and even the Nobel laureate, Tom Cech, independently proposed an identical hypothesis. The new vistas opened were awesome: Editing was now a type of RNA splicing and was a very ancient phenomenon indeed!
But then evidence slowly accumulated drip by drip that the chimeric intermediates were artifacts of cleavage ligation and that our original theory was correct and not the awesome transesterification model. Again a beautiful theory crashed on the hard rocks of inconvenient facts, but the inevitable low was tempered by the high that remained from the fact that our original model was indeed correct.
A few years have passed since those exciting days but the memories linger.
From Protist (2009) In press.
My personal epiphany
From Protist (2007) 158, 3.
Musings on the real problems
But the certainty of the universal devastation which will be, and amazingly, is already starting to be being reeked by human-caused climate change throughout this world of ours is to my mind the most serious and consequential problem that Homo sapiens has ever faced. The various scenarios modeled by the most eminent climatologists are frightening and bode ill for civilization as we know it now. The certainty of rises in ocean levels which will inundate island nations and flood costal cities world-wide, combined with the certainty of changes in weather patterns and sources of water have extreme consequential predictions. These changes will produce starvation, increase disease and cause massive emigration of millions upon millions of people world-wide. The eventual pressure on highly industrialized countries to decide whether to accept the massive immigration of poor starving people or to build Berlin-walls to keep them out and try to preserve their own devastated infrastructures and crumbling economic frameworks produced by the loss of major cities will be one of the most important ethical and moral decisions ever made. But the walls will be to no avail and this influx and the destruction of societies will forever change the industrialized societies in irreversible ways. An immediate result will be the use of military power to either obtain newly fertile regions for agriculture or to fight against the movements of peoples. The resulting wars will devastate more counties and weapons that were created never to be used perhaps will finally be used. Finally the economic and social framework and the very fabric of modern societies will collapse. The further consequences can not even be imagined by my feeble imagination.
Of course it is clear to anyone who can think rationally that the ultimate underlying cause of these horrible scenarios is overpopulation, which appears for multiple fundamental reasons to be impossible for the human species to change. But there are of course more immediate causes that actually can be remediated somewhat. A mandated world-wide severe decrease in the output of carbon dioxide from burning of fossil fuels would by all the models begin to decrease the rate of change, but this also appears to be beyond the abilities of humans (if our leaders and politicians are indeed human).
I myself will probably not experience the worst of this but our children and their children certainly will. Perhaps our species’ evolutionary time span has been reached, but I truly hope not. The intelligence, ingenuity and resourcefulness of humans will perhaps reverse these trends and leave the protistologists a little more time to study our little beasties.
From Protist (2009) 160, 1.
What is Science and Why do I do It?
From Protist (2008) 159, 3.
Tuesday, July 21, 2009
The Best of Times
From Protist (2002) 153, 365.
Death of the "ologies"
This compartmentalization was quite successful and led to the creation of many departments of “-logies”, each with a separate supposed set of goals that survive to this day in all major centers of higher learning. It also led to the creation of innumerable tenure-level jobs for Chairs, Directors, Deans and the like, each with their own fiefdom of administrators and budgets and also a few researchers or professors.
Generalizations and attacks on the status quo are dangerous and lead to shrill counter attacks by those affected, but I feel it is clear that the growth of modern science has led to the death of this venerable institution. Let me illustrate this in the field I am familiar with – modern biological research. Yes there are still Departments of Biology, Physiology and even Botany, Zoology and Protistology, but everyone in these Departments is doing the same thing and this has nothing to do with the ”ology” that pays their salary. They are studying interesting problems from every point of view at every possible level. The Protistologist, say, is interested in the motility of a particular protist. He or she however is interested in not only the molecular mechanisms involved down to the level of the molecules and energetics, but also the comparative aspects of motility in other related protists and even metazoans, the evolution and origin of this mechanism (and the cell itself), the morphological aspects, the natural history of this phenomenon, and even the role of this phenomenon in eco-communities of cells, and from a selfish anthropomorphic point of view, the possible biomedical significance, including the immunological aspect and interaction with the host if they are parasites. Each aspect of this study could be called by a different “ology” and therefore the existing nomenclature fails to communicate the existing reality.
One sign of the death throes of the “ologies” is the desire of almost all University Departments in the Life Sciences to include the word, Molecular, in their title. At my University, UCLA, it began with the creation of an interdepartmental Institute of Molecular Biology almost 42 years ago. Then the powerful techniques of molecular biology diffused to the existing “ology” Departments and there was a recurring scramble to rename the existing Departments and to wage the turf battles with the Institute that resulted. Even clinical Departments in the UCLA School of Medicine began hiring basic researchers who used recombinant DNA techniques and the great name change race was on. The final result as of today is that the venerable Molecular Biology Institute is a place where one eats a free lunch on Tuesdays while listening to seminars, and every Department is the same with a heterogeneous group of people all using every possible research technique ranging from molecular to organismal to ecological to study basic problems in the life sciences and biomedicine. But they still advertise themselves as different, claim to have specific goals and still teach courses with different names, but this is like whistling into the winds of change.
Another sign of the death throes is the emergence of entirely new fields derived from amalgamation of existing fields and exhibiting new “emerging properties”, such as, for example, Systems Biology or Astrobiology and the Search for Extraterrestrial Life. I myself find that I utilize examples in my courses of, for example, the discovery of dark matter and dark energy in the Universe from Astronomy as metaphors for the discovery of the World of Small RNAs in Biology.
I make no value judgment on this paradigm-changing change in academic organization, except to say that it makes life much more interesting but at the same time more confusing. Politicians, Universities, students and even faculty like compartments and get disoriented when faced with the chaos of real life. But perhaps the death of the “ologies” may lead to a deeper appreciation of the true goals of modern science and academics – an answer to the really big questions of what life is, where it came from and how it works, who we are and where we came from, and what is existence and the nature of things.
From Protist (2006) 157, 361
Who am I?
From Protist (2006) 157, 89.
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I have a suggestion for the siting of a large solar power plant in the Mojave desert: Use the Owens Lake bed, which is a 200 sq mile dry lak...
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As I have said before, the Republican Right has a policy of denying human-caused climate warming and even calling it a "hoax". The...
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I used to think that our Northern neighbor, Canada, was one of the most civilized (and civil) industrial countries. And then came Tar Sands...
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