greg goebel / public domain
* VECTORS is a newsletter of fact and commentary on aerospace, technology, science, and historical topics.
* This is the final issue of Vectors. There were a number of reasons to kill it off after all these years, but the primary one was that it was proving impossible to keep both the site blog and Vectors going simultaneously. I couldn't do both and so Vectors had to go.
Thanks for the attention. The "In The Public Domain" website will continue at the same level of effort; please check the site monthly for updates.
* The notion of "network distributed supercomputing (NDSC)", in which large networks of internet-linked personal computers contribute spare computing time to help tackle computation-intensive problems, has been around for some time. The pioneer was the famous "SETI@home" effort, begun in 1999, which used an NDSC system to analyze radio astronomy data for possible signals from other civilizations. SETI@home now has three million personal computer "nodes" in its network. It was followed by similar NDSC systems.
The idea has definitely caught on. NDSC is admittedly a limited tool: it is only workable for certain classes of problems in which the nodes in the network can be assigned a task list, told to crunch it out on its own, and then report back the results. One example is brute-force codebreaking, in which each node is handed a list of possible keys and told to check them out, then report if one works. NDSC is completely unworkable if the nodes have to trade data on the results of their calculations at each step; weather simulations and the like have to be performed on specialized supercomputers consisting of networks of processors datalinked closely together.
However, the list of problems for which NDSC does work turns out to be very long, and those interested in the technology are getting help from the "Berkeley Open Infrastructure for Network Computing (BOINC)", which provides open-source software for NDSC projects. BOINC was set up by David Anderson, one of the prime movers behind SETI@home, in 2002, and now over 40 BOINC projects are in operation. IBM Corporation is a big backer, operating a "World Community Grid" with 800,000 nodes that provides computing muscle for university projects such as "Help Conquer Cancer", "Discovering Dengue Drugs", and "AfricaClimate@home".
BOINC isn't just for the big shots, either. In 2005, an 18-year-old Lithuanian business student named Rytis Slatkevicius launched "PrimeGrid", an effort to create a database of prime numbers that has pushed beyond existing databases of primes. Slatkevicius funds the project through banner ads, donations, plus sales of the occasional t-shirt and coffee mug.
In addition, NDSC isn't just for PCs. A project known as "Folding@home", run by Vijay Pande and his team at Stanford University, performs analyses of the folding of complicated proteins using a network of Sony Playstation 3 game consoles. Folding@home has 40,000 game consoles in its network, providing a total computing power of 10^15 floating-point operations per second ("petaflops"), constituting one of the most powerful supercomputers on Earth -- when its nodes aren't running Sonic the Hedgehog.
Game consoles aren't simply a secondary resource. They are built around graphics processor unit (GPU) chips that are optimized for fast floating-point calculations, which it just so happens are what some NDSC applications, protein folding being a good example, are dependent on as well. A GPU can crunch such applications at least 50 times faster than a PC's CPU, and in some cases can be a hundred times faster. Sony was very cooperative in helping Folding@home figure out how to make use of the Cell processor on the Playstation 3 console, and even shipped some consoles with Folding@home software preloaded.
Along with the NDSC networks themselves, online support systems for network volunteers have sprung up, such as the GridRepublic portal. BOINC even operates a help desk using the Skype internet-telephony service. Volunteers have competitions, individually and in teams, to provide the most computing time on a particular project.
* In an interesting irony, volunteers are now providing NDSC computing power with the "meat computer" they carry between their ears. The "Galaxy Zoo" project was begun in June 2007 as a collaboration between astronomers at Oxford University and Portsmouth University in the UK, along with Johns Hopkins University in the USA. The objective was to use volunteers to classify galaxy structures picked up by the Sloane Digital Sky Survey, a project using a wide-field telescope to take high-resolution digital pictures over the sky. Computers can perform galaxy structure classification, but humans can do it much better. In a few months, 100,000 volunteers classified over a million galaxies. Plans are being made to extend the scheme.
There is nothing new about scientists making use of networks of amateurs to perform research; professional astronomers rely on amateurs to spot comets, and ornithologists make good use of "birders" to obtain data on bird migrations and populations. However, in those cases, the amateurs are often very knowledgeable, with years of experience that in some cases the professionals envy. In the case of NDSC-based research, anybody with a PC or networked game console can play, no matter how low their level of skill.
Finding volunteers hasn't been a problem; a few press releases in the right online outlets will generally yield tens of thousands of volunteers through simple word-of-mouth. The Galaxy Zoo project was overwhelmed by the response at first and had to upgrade its servers to keep up with the load. There is the issue of making sure the volunteers do the job right, but that hasn't been much of a problem, either. The Galaxy Zoo system obtains classifications for a particular image from over 30 different volunteers and performs a "majority vote" calculation to get the result; spot checking indicates that a professional astronomer couldn't do a better job. Some of the volunteers will even spot bugs in the system and recommend fixes.
One of the big obstacles is getting researchers to take the idea seriously. The US Stardust probe, which trapped microscopic particles from the "coma" around a comet in a glassy aerogel and returned them to Earth, left researchers with the need to hunt through the haystack of aerogel for the needles of particles. When Andrew Westphal of the University of California at Berkeley first suggested the idea of using an HDSC to perform the hunt, few of his colleagues were enthusiastic about the idea, but after "Stardust@home" went online in August 2006, 24,000 volunteers using a web-based "virtual microscope" performed more than 40 million searches and located 50 candidate dust particles, in some cases spotting faint tracks that would have been easily overlooked even by a professional researcher.
The internet is so vast that it is possible to find plenty of volunteers to support even the most dusty-sounding research efforts. For example, "Herbaria@home", run by Tom Humphrey of the Manchester Museum, effectively makes use of volunteers to document 18th-century plant specimens. A volunteer gets a digital image of a specimen along with the original notes, and then tranfers the information into an online database. Herbaria@home has catalogues 12,000 specimens so far, and the plan is to extend the effort into collections at other museums in the UK and elsewhere.
David Anderson has now launched a new open-source effort named "Berkeley Open System for Skill Aggregation (BOSSA)", the objective being to provide tools for "distributed thinking" along the lines of those BOINC provides for distributed computing. BOSSA is already being used on a program under the "Africa@home" NDSC effort in which volunteers will help to extract useful cartographic information -- the locations of villages, fields, roads, wells, and so on -- from satellite imagery covering regions where maps are out of date or nonexistent.
Others are starting to consider what can be done with game consoles to support distributed thinking networks. After all, people collectively spend billions of hours a year pouring effort into video games; it is tempting to get a slice of that resource through games that actually accomplish something other than destroying demonic invaders from another dimension.
* Charles Darwin famously came up with the notion of evolution by natural selection in his 1859 book THE ORIGIN OF THE SPECIES, providing an explanation of how organisms evolved from ancient forms of life through environmental pressures. His theory based on the notion that mutations will occur in new generations of a species, and that if these mutations provide the organism with an advantage in surviving or procreating, the mutant organism will increasingly dominate the population of the species. Darwin called this notion "natural selection", as a contrast to the "artificial selection" long practiced by plant and animal breeders.
Darwin had no clear notion of heredity, the scheme by which changes were passed down from generation to generation. An Austrian monk named Gregor Mendel did uncover the basic ideas of heredity in a series of experiments on pea plants, with the results published in 1865, but the paper went unnoticed until 1900, long after Darwin's death. Mendel is now honored as the founder of the science of "genetics", in which traits of an organism are passed on in discrete units known as "genes". Further work on the genetics of fruit flies nailed down Mendel's ideas, and by the 1940s biologists had been able to synthesize a modified theory Darwinian evolution that incorporated genetics. This revised theory was known as "neo-Darwinism" or "the modern synthesis", after the 1942 book EVOLUTION: THE MODERN SYNTHESIS, by British geneticist Julian Huxley.
However, though nobody doubted the existence of genes, nobody knew exactly how they were constructed. Evidence had accumulated that the genes were encoded in a molecule named "deoxyribonucleic acid (DNA)", found in the cell nucleus, but it wasn't until 1953 that Francis Crick and James Watson determined the structure of DNA and how it encoded genes. The DNA "double helix" molecule is made up of two long strands of chemical building blocks called "nucleotides", each containing one of four bases: "adenine (A)", "thymine (T)", "guanine (G)", or "cytosine (C)".
The four bases are organized in "triplets", allowing them to specify the twenty "amino acid" building blocks of proteins, as well as a few operating commands. A gene, essentially, consists of a sequence of DNA bases that allow it to define a particular protein. Most of the time cellular genes are inactive; when a gene is activated, its DNA is copied into a very similar molecule named "ribonucleic acid (RNA)" and then "translated" into protein.
The activation of specific genes was an interesting puzzle. There are about a hundred trillion cells in a human body, with each cell containing thousands of different types of molecules. All our cells have exactly the same "genome" or set of genes, but the cells themselves may vary widely in form -- nerve cells, skin cells, muscle cells, and so on -- with the different forms organized into a particular structure that makes up our body. It is the selective activation of the DNA in a cell that permits this elaboration.
* This process of selective gene activation remained poorly understood for decades following the discovery of the structure of DNA. Early on, there were also some deep misunderstandings of the operation of genes. It was known that mutations in DNA gave rise to the variations in organisms that, along with natural selection, drove evolution; and the assumption was that relatively recent and elaborate evolutionary "innovations", such as humans, would have much more complicated genomes than ancient and relatively simple organisms, such as parasitic nematode worms. However, by the end of the 20th century a number of genomes had been deciphered, with the human genome decoded a few years later, and the results were startling. Humans had been expected to have about 60,000 genes, but the count was only about 30,000. Nematode worms have about 14,000 genes.
Actually, this did not come as a complete surprise, since even before the era of genome sequencing, molecular geneticists had been obtaining hints as to the structure and operation of genomes. The first genetic control was discovered by Jacques Monod and Francois Jacob in 1961 in the human colon bacterium, Escherichia coli.
The E. coli bacterium normally lives off the sugar glucose, but can also produce an enzyme -- catalytic protein -- to digest the milk sugar lactose. How does the entirely brainless bacterium know when to switch on the genes to make "lactase", the lactose-digesting enzyme? What the two researchers discovered was that a protein called a "repressor" is normally attached to the beginning of gene that produces lactase, blocking replication. If the bacteria then encounters lactose, the lactose binds to the repressor protein and detaches it from the gene, allowing production of lactase. The repressor protein acted as a molecular "switch" to turn lactose production on or off.
Since only a fraction of the complement of genes present in a cell are turned on, or "expressed", at any one time, Monod and Jacob suggested that other genes must be turned on or off in much the same way. They didn't have absolute proof that was true, but it was a very attractive theory; as Jacob wrote later:
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It proposed a model to explain one of the oldest problems in biology: in organisms made up of millions, even billions of cells, every cell possesses a complete set of genes; how, then, is it that all the genes do not function in the same way in all tissues? That the nerve cells do not use the same genes as the muscle cells or the liver cells? In short, [we] presented a new view of the genetic landscape.
END QUOTE
There was a greater significance Monod-Jacob model of gene function, but it would take about two decades for it to become apparent. Certain sorts of birth abnormalities had been known since antiquity, for example animals with two heads, or an auxiliary pair of legs, and so on. Such abnormalities looked like a plan of some sort gone wrong, as if the instructions to build a head or a pair of legs had been duplicated, but it wasn't until the development of modern biology that the matter began to be investigated in any detail. In 1894, the English biologist William Bateson published the book MATERIALS FOR THE STUDY OF VARIATION, which catalogued abnormalities that he observed in insects and other animals -- for example, a mutant fly with a leg instead of an antenna on its head, and mutant frogs and humans with extra vertebrae, what he called "homeotic" mutants. He believed such "macromutations" challenged Darwin's idea that evolution was gradual.
The precise nature of these particular macromutations wasn't understood until the late 1970s, when studies by Edward Lewis of the California Institute of Technology (CalTech), Christiana Nuesllein-Vollhard and Eric Wieschaus in Germany, and others showed that these abnormalities were caused by mutations of a particular set of genes in fruit fly embryos that controlled development of the fly's body and the distribution of its attached appendages. Very similar sets of genes, exercising much the same kind of controls, were soon found in nematode worms, flies, fish, mice, and humans.
These genes operated by much the same principles as discovered in Monod and Jacob's repressor molecule. Eight of these controlling genes, known as "Hox" genes, are found in all animals and are estimated to have been around for a half billion years. Fruit flies and worms have a single set of Hox genes, while fish, reptiles, birds, and mammals have four sets. An animal embryo originally looks like a simple ball; the Hox genes selectively produce Hox proteins to gradually shape the proper form of the animal, converting the simple embryo into a more complicated structure with distinct compartments, and then directing the assembly of components in each compartment.
The Hox genes, importantly, do not specify the actual structure of a component, they simply control the overall layout of the components that make up the organism. The Hox proteins operated in a way very similar to that of Monod and Jacob's repressor molecule, turning other genes on and off, in essence controlling the "routines" that create various body components.
Hox proteins behave in this way because of a particular genetic feature of the Hox genes that produce them. Within their genetic composition, all eight Hox genes possess a nearly identical section of DNA, called a "homeobox", as a tribute to Bateson. When Hox genes produce Hox proteins, the homeobox region of the Hox genes carries the genetic information to produce a specific part of these proteins called the "homeodomain". Once the protein is assembled, its homeodomain attaches to DNA sites that control genes, allowing it to function as a switch.
There are other developmental genes beside the Hox genes -- for example a gene known as Pax-6 that controls the development of an eye. If the Pax-6 gene is damaged in a fruitfly, it won't develop eyes. Interestingly, a Pax-6 gene from one animal can be exchanged for the Pax-6 gene in the genome of a second animal, and the second animal will develop normally. A Pax-6 gene from a mouse will produce eyes when spliced into a fruitfly. In fact, the development of legs, wings, arms, fins, and so on are all under the control of virtually identical genes and, as with the Pax genes, in many cases are interchangeable.
The commonality of developmental genes between distantly-related species was not at all a surprise to biologists, since it was consistent with Darwin's notion of the common descent of species from common ancestors. What was a surprise was that all animals are so genetically similar. Darwinian evolution is driven by mutations; now it turned out that even minor mutations could account for massive changes in form, and that wildly different animals could be produced by fairly modest changes in developmental genes. For example, consider the neck of the giraffe. It has seven cervical vertebrae, the same as all the other mammals, but they're longer. Hox genes control not only the number of vertebrae, they also control cell proliferation and so the size of the vertebrae. That means that the longer neck could have resulted from a simple mutation in the giraffe's Hox genes.
Evolution depends mostly on alterations of patterns of gene regulation, not on the creation of new genes. The actions of genes are complicated, with the characteristics of an organism generally depending on the cooperative action of multiple genes. There is no one gene for an eye. Genes are like words that make up sentences whose meaning depends on the context. In the modern vision of "evolutionary development" or "evo devo", the words and to an extent the sentences are common among many organisms, and so they are not as unique under the skin as they appear. Spiders, centipedes, reptiles, birds, mammals, all become variations on a common theme.
The identification of master developmental genes also helps ensure that changes to one feature of an organism have a degree of independence from changes to other features. A dachsund, for example, is a dwarf, a dog with a normal-sized body but short legs, originally bred to chase badgers down holes. It would have been more difficult to come up with a dachshund if a mutation had required for each leg, and the mutations had other major effects on the dog. In reality, a developmental gene mutation commanded: GROW SHORT LEGS -- and so it happened.
Similarly, snakes evolved from lizards through developmental mutations that got rid of the limbs and extended the body, rib by rib. It wasn't a question of having to evolve a completely new design; the snake retains other lizard subsystems more or less unchanged. The genetic changes from lizard to snake are now seen as much simpler and fewer and number than they would have in, say, the 1970s.
The current belief is that developmental genes are only one aspect of the "core processes" that direct the construction, growth, operation, and behavior of organisms. They still remain generally mysterious, but the expectation is that in their full revelation they will make up a comprehensive "toolkit" for organisms, with different species seen as merely different applications of the same common elements.
* DROPPING THE BOMB: During the spring of 1945, facilities for handling atomic bombs -- including an air-conditioned assembly facility and pits to allow the oversized bombs to be winched up into bombers -- were built on Tinian, with Tibbets' 509th Composite Group arriving in early June to prepare for action. The group was equipped with the latest B-29s, featuring improved engines, a lighter airframe, and a number of technical improvements. The crews practiced by flying to Iwo Jima and back, as well as bombing isolated Japanese island garrisons using ordinary general-purpose bombs and, later, pumpkins. Curt LeMay talked with Tibbets on plans for dropping the atomic bomb, the general saying that a low-level attack would be more accurate than a high-altitude drop. It seems that LeMay didn't quite understand what an atomic bomb could do; Tibbets made it clear that a low-level drop was neither necessary nor attractive.
The political wheels were turning towards the go-ahead for operational use of the atomic bomb. War Secretary Stimson knew the Japanese would resist an invasion of the home islands with absolute determination, but he did not accept the popular propaganda of the time that painted the Japanese as what he described as "mad fanatics of an entirely different mentality than ours." Stimson was aware of how rapidly the Japanese had moved from feudalism to a modern industrial society, and regarded them as both intelligent and pragmatic. Given the dire condition of Japan, Stimson thought that it would be sensible to send them an ultimatum, which would say that worse was coming but also provide reassurances concerning the all-important status of the Japanese Emperor.
By late July, Hiroshima was clearly at the top of the target list. On 26 July, the same day the cruiser USS INDIANAPOLIS arrived at Tinian with its atomic payload, the Allies issued an ultimatum to the Japanese, calling on them to surrender. It promised that, following occupation and demilitarization, Japan would become a free and independent democracy. Nothing was said one way or another about the status of the Emperor, the consensus being that it might encourage the Japanese to keep on fighting harder in hopes of getting a better deal. The next day the Japanese make it clear they were not willing to accept.
On 30 July, authorization was given to drop Little Boy on Hiroshima. The day before, 29 July, in one of the uglier stories of the war, the INDIANAPOLIS was torpedoed by the Japanese submarine I-58 in the Philippine Sea. The cruiser promptly went to the bottom. That wasn't the truly ugly part of the story; such misery is common in war. The ugly part was that, due to a ghastly bureaucratic screwup, nobody noticed the INDIANAPOLIS was missing for almost four days, during which time hundreds of sailors who might have been rescued drowned as their life vests became waterlogged, or were attacked by sharks, or went delirious for lack of water.
* On 6 August 1945, Paul Tibbets took a Superfortress, named ENOLA GAY after his mother, off the runway at Tinian. It was bearing the Little Boy bomb and its target was Hiroshima. It was joined by two other B-29s, one an observer aircraft, the other a photo plane. When they arrived over the city at mid-morning, no great attention was paid on the ground to the intruders, since a serious attack on the city would have required a much larger force. The three bombers were judged likely to be on a reconnaissance mission.
At 9:15 AM, ENOLA GAY released its warload. At a predetermined altitude, a set of radar-based sensors set off the bomb, which detonated in a explosion rated at about 11 kilotonnes of TNT, orders of magnitude greater than that of any bomb ever used in war up to that time. The aircraft were hit by two hefty shockwaves, one directly from the blast and the other reflected from the ground. A huge mushroom cloud swelled up over the city. The weapon achieved destruction with a flash of incandescent energy, including high-energy radiation, and an explosive blast wave; buildings were smashed and fires sprung up over the city in an instant. The city center was levelled, tens of thousands of Japanese were killed immediately, and those on the edges of the blast were hideously burned or injured by debris. The radiation from the blast long-term environmental and public health damage.
The success of the attack on Hiroshima was promptly reported back up the chain of command. Les Groves called from Washington DC to tell Oppie the news: "I'm very proud of you and all your people."
Oppenheimer asked: "It went all right?"
"It went with a tremendous bang." Oppenheimer expressed satisfaction; when Leo Szilard got the news, he expressed anger, calling one of the "greatest blunders in history." To the surprise of some, the Japanese didn't surrender immediately. One of the difficulties was that Hiroshima had been so totally destroyed, with all communications disrupted, that it was hard for Tokyo to figure out what had happened. Japanese civilian leadership felt the destruction of Hiroshima meant that there would be no shame in surrender, but the military still wanted to fight to the last. B-29s dropped leaflets over Japanese cities announcing what had happened to Hiroshima and said that Japan had to surrender or face more such attacks.
It wasn't an empty threat. On 9 August 1945, B-29s paid a similar visit to Nagasaki, with the B-29 BOCK'S CAR dropping the Fat Man bomb. Fat Man, which was essentially a production version of TRINITY, was well more powerful than Little Boy, but Nagasaki was a hillier target and the damage was not extensive. The destruction was still immense. Truman didn't want to drop more bombs for the moment, preferring to keep up conventional incendiary attacks while the Japanese thought things over.
The Japanese military still refused to quit, but the Emperor finally decided to exercise the authority he held but up to that time would not use. On 14 August he asked his ministers to draw up an edict announcing the surrender of Japan to the Allies, while a message indicating the desire to surrender was passed on to Allied diplomats through Switzerland. There was an attempt at a military coup to intercept the surrender, but the insurgents were suppressed and the Emperor's will prevailed. He read the edict to his people on 15 August, asking them to "bear the unbearable." World War II was over.
* THE END OF THE BEGINNING: The fighting was over, and for the moment the pressure was off. The Axis had been crushed, American soldiers were coming home in floods and demobilizing, America was literally throwing weapons away, in some cases flying brand-new combat aircraft straight from the factory to the scrapyard.
By September 1945, most of the physicists who had worked on the atomic bomb project were going back to peacetime work; Fermi, only half joking, suggested that it was time for scientists to figure out a cure for the common cold. The only serious activities going on at Los Alamos for the time being were packing up, saying goodbyes, and leaving. The lab would stay in business over the longer term, but its staffing abruptly fell in half, and it would no longer be a concentration of the scientific elite.
Although the US was in retreat from its wartime posture as a military superpower, the Soviet Union was not. Despite his seeming indifference to Truman, Josef Stalin had found the American development of the Bomb disturbing, particularly because they had actually used the thing. If they used it once, they would almost certainly use it again. Now that Hitler was dead and the Americans were arming themselves with nuclear weapons, the Soviet atomic bomb project went from an investigation effort to a full-blown development program. With Hiroshima, Stalin had got the message and the atomic bomb development effort went to the absolute top of the priority queue, taking precedence over rebuilding the USSR's shattered cities. Soviet citizens might go homeless and hungry, but the Soviet Union would have an atomic bomb, regardless of the expense or environmental damage.
Late in 1945, the US embassy in Moscow passed on leaks that the Soviets did have an atomic bomb development program in progress. There was, however, a tendency to regard the USSR as more backwards than it really was. A joke made the rounds that the only way the Soviets could attack the USA with a nuclear weapon was by smuggling it in using a suitcase -- but then they'd have to refine the suitcase first.
The Americans had greatly overestimated the German capability to build an atomic bomb, and now went to greatly underestimating the Soviet capability to develop such a weapon. As Leo Szilard had taken pains to point out, there was nothing magical about a nuclear weapon: if one nation could build it, in principle so could another. Kurchatov's group included world-class scientific minds and the Soviets were capable of mobilizing massive industrial resources. Very significantly, they also had almost all the information they wanted on the American atomic bomb program: there were at least three Red spies inside Los Alamos. The most important of the trio was Klaus Fuchs, who passed on plans of the Fat Man bomb to the Soviets. Although Soviet physicists believed they could design their own atomic bomb, given the extreme pressure to get results, the easiest thing to do was to just copy the Fat Man bomb.
* In early 1948, the US was served notice that hopes for a peaceful postwar world order were unrealistic. Stalin ordered a blockade of Berlin, cutting off power and ground access to the city. The US and Britain organized an airlift to resupply Berlin by air, with transport aircraft arriving in precisely-planned schedules every few minutes over a period of eight months. Stalin had been outmaneuvered, given a taste of the material power of the Americans. He chose not to escalate the confrontation by interfering with the airlift.
By the summer of 1949, Kurchatov and his researchers went to the steppes of Kazakhstan to complete preparations for the first Soviet atomic bomb test. It took place in August. The blast was kept a secret, but not long before the shot some American researchers had been prudent enough to suggest that Soviet nuclear activities needed to be monitored, even though the conventional wisdom was that the USSR wasn't close to developing a bomb. An organization was set up to do the monitoring. Following the test, a B-29 carrying air filter systems picked up the airborne radioactive fallout from the test. After checking the samples carefully, on 24 September 1949, the Americans announced that the Soviet Union had detonated an atomic weapon. The announcement caught Stalin completely off guard. He had believed the secret could be kept, and the detection of the blast was another unsettling bit of evidence of the technical lead of the West, though in fact the Americans would have missed it if it had occurred much earlier.
If the Berlin blockade had been a wakeup call, the Soviet Bomb was a fire alarm. America had to mobilize to deal with the threat by all means short of an all-out shooting match. This state of belligerent armed peace would acquire a name: the Cold War.
* Both sides went on to stockpile atomic bombs and go on to develop fusion bombs: Edward Teller's super bomb became a reality. Both sides tried to prepare their citizens for a nuclear war. The Eisenhower Administration sensibly concluded that there was no way shelters would be effective against the H-bomb, and plans were made for mass evacuations instead. Exercises and simulations were conducted in which US cities were "attacked" and the results of preparations were evaluated. The results, even on paper, were grim, but the administration believed that the civil-defense preparations were valuable anyway, to help prevent the civilian population from panicking under attack. Despite the corny propaganda films of the time, the leadership had few illusions about the severity of a nuclear exchange.
Nobody really believed there was any way to win a nuclear war. The name of the game was "deterrence": to make certain the Soviets understood that if they attacked the US, they would all die as well. Of course, it worked the other way as well. The policy acquired a name, "mutual assured destruction", with an acronym whose irony was obvious to all: MAD.
In the 1970s, the Nixon and Carter Administrations would take steps to scale back the arms race, but a hardening of positions between the superpowers led to the rise of Ronald Reagan, the idol of the conservative Right. Ironically, it was Reagan who, after beginning a surge in weapons procurement, drove significant arms-control treaties between the US and the Soviets. By the early 1990s, the Soviet Union had collapsed, and the Cold War was over. Nuclear weapons still remained a threat to peace, but the days when the superpowers were poised to annihilate each other were over.
END OF SERIES
* GOULD & PUNCTUATED EQUILIBRIUM: Stephen Jay Gould became one of the most high-profile evolutionary scientists, his books often making the best-seller lists and leading to appearances on talk shows. His high public profile led some of his colleagues to regard him as more of a science writer and self-promoter than a scientist. Like Dawkins, Gould was inclined towards controversy, and working with Museum of Natural History paleontologist Niles Eldredge (born 1943), he produced it in quantity by proposing what became known as "punctuated equilibrium".
Even Darwin had noted that the fossil record was inconvenient to Darwinism in some ways, suggesting that though there was a clear succession of forms, species seemed to remain stable for long periods of time. For example, the oldest known fossil of a bat is about 50 million years old and is a perfectly respectable bat. Darwin chalked this up to the sketchiness of the fossil record, and most after him maintained that notion, remaining committed to his notion of evolution by slow steps or "gradualism". Bats, for example, are small, relatively fragile, tend to live in environments where fossilization doesn't happen often, and accordingly fossil bats are very rare. What Eldredge and Gould proposed was that the fossil record was correct as known: that species went through rapid bursts of evolutionary change and then settled down to a fairly static existence.
The quarrel over punctuated equilibrium became loud and noisy, but it seems only because it was made to be. Gould and Eldredge presented their case as if it were revolutionary, and their critics accused them of trying to overthrow neo-Darwinism, mocking punctuated equilibrium as "evolution by fits and starts". Some were ruder, calling it "evolution by jerks" -- with Gould shooting back at his adversaries, referring to "evolution by creeps". Critics of Darwinism in general unsurprisingly jumped into the fray, claiming it proved that evolutionary science really was in a state of complete disarray and confusion.
In reality, the idea that species would emerge through rapid change and then settle down to a relatively static existence was nothing new, having actually been proposed by the unbelievably thorough Darwin in the fourth and later editions of THE ORIGIN OF SPECIES:
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Many species once formed never undergo any further change ... and the periods, during which species have undergone modification, though long as measured by years, have probably been short in comparison with the periods during which they retain the same form.
END QUOTE
Darwin strongly emphasized that natural selection only works in a gradual way, but he didn't mean that it worked at the same rate at all times in the history of a species. 100,000 generations is plenty of time to obtain considerable evolutionary change through gradual changes screened by natural selection; after all, that's a near-invisible change of a thousandth of a percent per generation. Given a fairly ordinary small organism with a generation time of a year, 100,000 generations is only 100,000 years. Most people would be incredulous at that phrase "only" 100,000 years, since that's a vast interval by human standards, twenty times longer than recorded history -- but it almost doesn't register in the geological record. It's effectively instantaneous.
Even a million years is a relatively short time by geological standards, but a million generations could result in massive changes in organisms. Imagine a video of the successive generations of an organism along a continuous line of its evolution, with one frame per generation and a reasonable video rate of 30 frames a second. The whole video would last over nine hours; we would certainly be able to see visible changes in time scales of a minute -- 1,800 generations -- and expect to see considerable transformations in an hour -- over 100,000 generations. The organism in the final frame could easily be "morphed" all out of recognition from the one in the first.
Could natural selection create a modern bat from a completely flightless ancestor in a few million years? As far as Darwinism's concerned: sure, why not? In fact, as Gould and Eldredge pointed out, as far as Darwinism's concerned, it would be baffling if it took tens of millions of years, since that would imply selection pressures so very low, adaptive changes in organisms in invisible millionths per generation, that they would be lost in the noise. There's every reason to expect that the evolution of a particular adaptation should be rapid, at least by the generous notions of the geological timescale. The interval between an australopithecine and a modern human is only about three million years, but over that time the brain size almost tripled -- an adaptation that produced our biological supercomputer, as or more dramatic as the bat's development of flight. Conservatively assuming an average generation time of 25 years, three million years is only 120,000 generations.
Furthermore, a notion that evolution might take place rapidly in small, isolated branch populations of a species went back to Sewall Wright, and Ernst Mayr had suggested in his founder principle that such isolated populations might quickly evolve and then displace their large parent populations in short order, at least on geological terms. In this view, the evolutionary progression of the branch species not only took place with relative rapidity, it took place off the main stage in a small population -- meaning the odds of finding transitional fossils would be low, while the odds of finding fossils of the stable main population would be high. The transition from one species to the next would seem, in geological terms, instantaneous.
Not all evolutionists thought much of the founder principle, but Gould and Eldredge actually had it as part of their brief and knew it wasn't news. They were accused of going back and forth over their ideas, stressing their radicalness, to then retreat in the face of loud criticisms -- plus the inclination of outsiders to try to hijack the controversy -- and say there was nothing really radical about them at all.
* It is easy to exaggerate the disputes of academics. There are likely to be differences of opinion on matters great and small in any field of endeavor, and though the disputes may be polite, with wagers placed between friends, some people don't know how to express the slightest difference of opinion except as a quarrel. Academics -- of any persuasion, not just the science faculty -- may conduct bitter lifelong conflicts over matters so petty that outsiders can't even figure out what the fuss is about, along the lines of the wars of the Liliputians in Jonathan Swift's GULLIVER'S TRAVELS, with "Big-Enders" and "Little-Enders" murderously fighting it out over which end of a soft-boiled egg to break. Swift was specifically mocking religious crusades, but as a college dean he was only too familiar with the Liliputian quarrels of academics as well.
Even then, the fighting's more smoke than fire. As has been said in another context: if they were serious, they'd kill each other. Certainly it was a hoax for critics to cash in on the dispute and claim evolutionary science was in a state of complete chaos. The sciences are always learning something new and so necessarily work by a process of "successive approximation" towards a more satisfactory view of the real Universe, with ever finer details being argued and resolved. If the disputes of evolutionists were diverging from a consensus instead of converging towards one, there would be a problem -- but though there was a time when that was the case, it hasn't been so since the end of the First World War.
In hindsight, the whole feud over punctuated equilibrium was never any more than a tempest in a teacup. To the extent that there were issues, they were simply a debate among the evolutionary science community over details, and of no particular interest to outsiders. Why it became such a public dispute seems to have been a matter of the personalities involved, and the inclination of the popular media to play up the dispute.
* THE GENOMIC REVOLUTION: While evolutionary biologists debated and refined their game strategies, biochemists continued to probe the molecular basis of life. It wasn't until the late 1960s that the evolutionary biologists and biochemists began to interact: before that, the two groups had been isolated or, in some cases, even hostile to each other.
One of the problems was that though biochemists had cracked the genetic code in principle in the 1950s, they really couldn't obtain much leverage off their knowledge early on. Even in the mid-1960s, they still lacked the tools needed to actually read the genetic messages encoded in DNA. Traditional chemical analysis was largely useless for this task, since it could not give information on the specific sequence of base pairs in DNA.
By the end of the decade, biochemists had finally been able to isolate a single gene, and then synthesize a single gene. Using "restriction enzymes", by the early 1970s they were able create "recombinant DNA" -- that is, DNA featuring sequences spliced together from several different sources -- and insert a new gene into bacteria. These experiments established the basis for the two fundamental recombinant DNA techniques of "cloning" and "sequencing". In cloning, genomes were chopped into segments with restriction enzymes, and then the segments were spliced into the bacterial cells, which then produced the protein specified by the foreign genetic sequence. When a bacterium with a foreign genetic sequence reproduced by fission, it duplicated its new genetic sequence as part of its genome. Further generations of fission led to a population of identical "clones".
A number of techniques were developed to then obtain the sequence of bases in DNA by researchers such as Fred Sanger (born 1918) and Walter Gilbert (born 1932). Initially, deciphering even small genes took a good deal of time and effort, but the technology improved rapidly and soon biochemists were able to decipher important genes of the human genome.
The logical next step was to decipher the entire human genome. A rough map was available by 1987, but this was a simple task compared to the full decoding of all 3 billion bases in the human genome. The task seemed impossible for the technology at that time. Initially, work focused on fully deciphering simple genomes, such as those of bacteria -- with a few million bases -- by breaking the bacterial genome into random fragments, sequencing each fragment, and then merging the results. After acquiring experience, it seemed more likely that ongoing improvements in sequencing technology made the prospect of decoding the human genome more plausible, and after a few years of discussion and preparation, the "Human Genome Project" was formally initiated.
The Human Genome Project was formally launched in 1990. Although there were fears that the hoped-for improvements in sequencing technology wouldn't materialize, the human genome was finally deciphered in 2001. By that time, the genomes of a number of other organisms had been deciphered, and the list is now growing rapidly.
The improvements in our knowledge of our genome and the genome of other organisms are already having a great impact on biomedical practice. Our increased understanding of genetics has also already led to elementary "genetic engineering" efforts, involving the splicing of genes into crop plants and domestic animals genes from other, sometimes wildly unrelated organisms. Such "transgenic organisms" include cowpox viruses modified to generate coat proteins from dangerous pathogens to provide safe vaccines; bacteria that have been spliced with the human gene for insulin, allowing the production of insulin in greater quantities and at lower cost than earlier techniques; crop plants such as corn that have been spliced with genes from bacteria that produce natural pesticides; and domestic animals such as cows and goats that have been spliced with genes for human hormones, allowing these valuable hormones to be "harvested" from their milk.
* The deciphering of genes had a direct and major impact on evolutionary science. Traditionally, evolutionists had classified relationships among living creatures through studies of their morphology, but the patterns of genetic sequences in the genes of different organisms provided a much more accurate evolutionary map, confirming the broad lines of evolutionary development, but also showing that some relationships had been misunderstood. For example, until recently zoologists had thought that large dogs were descended from wolves and small dogs were descended from jackals, but genetic analysis showed that the genomes of even pekinese and yorkshire terriers closedly matched those of wolves. It is now clear that all domestic dogs are descended from wolves. Furthermore, there turned out to be patterns in genes that were common, with minor variations, among all organisms and could be used to trace out the patterns of descent and modification.
The deciphering of genes and the creation of transgenic organisms has also revived many of the old worries about eugenics. It is now possible to detect a number of latent hereditary illnesses in a genome, and such analyses are used in genetic screening. Couples who want to marry and have children can be screened to see if they carry any genetic defects that would pass hereditary afflictions, such as Tay-Sachs disease or sickle-cell anemia, on to their children. If they do, they don't get married to each other, or they adopt children instead.
A hard-core eugenicist might insist that people who have such genetic defects shouldn't have children at all, so those defective genes can be eliminated from the gene pool. In fact, most people have a number of potential genetic defects in their genomes, and such abstinence would mean the end of humanity. Genetic screening does pose some sticky issues -- for instance, insurance companies might try to set premiums based on screening results -- but there's no reason to fear the imminent return of eugenics laws. Such notions remain in exile among the lunatic fringe.
However, genetic technology gives us the long-term prospect of eugenics that actually works. The idea of genetically-modified humans is popular in science-fiction stories. Robert Heinlein moved on from his early notions of eugenic selective breeding and created a genetically enhanced superwoman in his popular 1982 sci-fi novel FRIDAY. Hollywood star Jessica Alba got her ticket to stardom playing the genetically engineered warrior Max in the 2000:2002 sci-fi TV series DARK ANGEL. (Max had a number of cat genes, which made her extremely agile, but also occasionally had some odd influences on her behavior.)
At the present time, the notion of a "designer baby" remains science fiction. Our ability to manipulate the genome is at a "stone axe" level of development and it's completely out of the question to create a genetically engineered human being. The technical obstacles to doing so are enormous, and if the time comes when it seems practical, tinkering with something as complicated as the human genome will have a drastic potential for unforseen side effects. Who's going to step forward to volunteer their kids to be first?
Still, in principle the time is likely to come, sooner or later, when humans will be able control their genetic destiny. This obviously presents dangers, but it is also going to be very hard for parents to resist the idea of having children who are healthier, stronger, smarter, and live longer. Evolution to this time has been a blind process; now we are faced with the prospect of being able to direct evolution. The bottle has been opened and the genie will emerge, like it or not. The matter's going to need some consideration.
END OF SERIES
* Website additions for the month include:
Updated documents include:
New reviews include:
This last month's online blog entries include items on: aviation infrastructure, Florida road trip. relationships among the cat family, materials harder than diamond, Morton's demon, US space exploration policy reconsidered, huge extinct rodent, free-space optical datalinks, changes in car sales, rivalry between the Bible & the Koran, the disastrous eruption of Laki in 1783, obtaining methane from depleted oil fields with bacteria, the organizational & financial challenge of developing video games, and the evolution of pygmies.
Online update links at: http://www.vectorsite.net/update.html