Hand Surgery Philosophy

The hand of the human being is probably the most intriguing and complex engineered bio-advanced miracle known to the human mind. It is therefore not hard to believe in the theory that the brain has developed secondary to the hand. The wealth of sensory input from the hand has been feeding the brain and creating millions of new pathways and synapses that have advanced the human brain beyond our comprehension. The human hand has the ability to grip an object in the palm, but even more so it has the ability to pinch. The pinch grip has been made possible by the thumb that can move in all directions (circumduction) and can hold objects against the index finger. The ability to hold something between your index or even little finger and thumb is truly the most advanced form of life and a miracle!

So when this miracle has been crippled by an injury, pain or chronic disease, the person suffers a great deal. But even more than just a state of suffering, a sense of loss and disability tends to cripple the mind as well. People only realise the multitudes of functions and the need for the hand in all activities of daily living, once it is injured, crippled by arthritis or immobilised for any reason.

Surgery of the hand is rather complex. It deals with pain, loss of function, delicate anatomy, complex biomechanics and to some extent, an intuition or understanding of the complexity of the real problem beyond what is commonly presented. This intuition is probably all about real listening to the patient and then to listen again. The solution is not always clear at first and might never be. The solution is not always surgery. The solution might be intensive hand therapy or sometimes rest from sport, work or even a long holiday. When the solution is surgery, in selected cases, the hand surgeon needs to apply all the foundations of the anatomy and patho-anatomy (when the anatomy goes wrong) and combine it with the art and skill of combined orthopaedic (bone and joints) and plastic (soft tissue) surgical principles to make the patient better. This can be a hard job, but with meticulous attention to detail and application of basic principles, it can bring great relief.

Please share your ideas and ideologies with us. We learn a great deal from patients and we will be delighted to hear from you.


Tuesday, September 26, 2006

Vanishing Military Historians

John J. Miller (via PDTR) investigates why military historians are become scarce on college campi. He quotes Mary Habeck, a military historian at the School of Advanced International Studies (SAIS) in Washington, D.C., who blames the "tenured radicals" of the 1960's, who prefer studying "the kind of social history [they] want to support." Thus, according to Miller, these academics concentrated on social history instead of "diplomatic, intellectual, and maritime history — but perhaps none have suffered so many casualties as the 'drums and trumpets' crowd."

Miller has surveyed American colleges and universities and explains:
At first glance, military history appears to have maintained beachheads on a lot of campuses. Out of 153 universities that award doctorates in history, 99 of them — almost 65 percent — have at least one professor who claims a research interest in war, according to S. Mike Pavelec, a military historian at Hawaii Pacific University. But this figure masks another problem: Social history has started to infiltrate military history, Trojan Horse–style. Rather than examining battles, leaders, and weapons, it looks at the impact of war upon culture. And so classes that are supposedly about the Second World War blow by the Blitzkrieg, the Bismarck, and the Bulge in order to celebrate the proto-feminism of Rosie the Riveter, condemn the national disgrace of Japanese-American internment, and ask that favorite faculty-lounge head-scratcher: Should the United States have dropped the bomb? “It’s becoming harder and harder to find experts in operational military history,” says Dennis Showalter of Colorado College. “All this social history is like Hamlet without the prince of Denmark.”
Miller also gives examples of endowed military history chairs that are going unfilled (University of Wisconsin); accomplished military historians who are retiring and not being replaced (Gerald Linderman and John Shy at Michigan); or replaced by non-military historians (James MacPherson's prospective replacement at Princeton is an expert in gender studies); and institutions that are refusing endowments for a military history chair at all (Dartmouth).

It's not just the universities that have turned away from military history. At least one of the mainstream historical scholarly publications has been ignoring straight military history, too.
Another reason for the shortage of scholars is that military historians have been shut out of The American Historical Review, the most prestigious academic journal for history professors. Last year, John A. Lynn [who states he is a Liberal Democrat--ed.] of the University of Illinois surveyed the last 150 issues of the AHR, which comes out five times annually. During this 30-year period, he couldn’t find a single article that discussed the conduct of World War II. Other ignored wars included the American Revolution and the Napoleonic Wars. There was a single article on the English Civil War, dealing with atrocities committed therein. Lynn located precisely two articles on the U.S. Civil War. One of these also dealt with atrocities. “I guess military atrocities are attractive to the editors,” he says. The only article on World War I focused on female soldiers in the Russian army. “I suspect the editors liked it because it was about women, not because it was about war.” The lead article in the most recent issue of the AHR is about wigs in 18th-century France.
Miller does qualify that the military academies are still strong in military history and also menitions that some public universities, including Kansas State, Ohio State, and Texas A&M, have strong, well-respected military history programs. However, he also explains that military historians are forced to find refuge at second-tier schools and in the military itself.

Miller may seem a bit snarky towards the social historians, but the point of his article isn't so much to attack what is being studied as it is to call attention to what isn't. Military history--traditional military history--is important because of the lessons it teaches:
“Knowledge of military history is an essential prerequisite for an informed national debate about security and statecraft,” says Michael Desch, a political scientist at the Bush School of Government and Public Service in Texas. Many voters, for instance, don’t know how to contextualize the nearly 23,000 U.S. military casualties in Iraq since 2003. That’s a pretty big number. But it’s also roughly the level of casualties suffered at Antietam in just one day, and a small fraction of the more than 200,000 casualties endured in Vietnam.

Critics of the war also have plenty to gain from a public that has a better understanding of older conflicts. “People might have realized that we have a poor track record of using the military to do nation-building in Third World countries,” says Desch. “The model isn’t Germany or Japan, but Nicaragua and the Philippines.” Finally, the population of Americans who have served in the military is shrinking, and with it their knowledge of what armies and navies do.

Anybody who has studied the history of war knows that it’s possible to snatch victory from the jaws of defeat — it happened at Shiloh, when a Confederate attack nearly routed the Union army, only to have General Grant drive them off the field of battle the next day. Perhaps military historians can stage a similar comeback. In their efforts to do so, they will be wise to remember something that Grant didn’t know back in 1862: An awful lot of brutal fighting lies ahead.
I think Miller's concerns about the dearth of military history courses offered to, say, your average undergraduate, is--while not unfounded--a bit overwrought. I can only point to my own personal experience.

I took courses titled "World War II" and "The Civil War" in which I think it could be reasonably expected that "military history" would be covered. In my World War II class, the professor (whom I'd describe as a diplomatic/social historian) came right out and said he wasn't going to focus on tactics (which was fine by me). Nonetheless, he did cover basic strategy and also touched on the "war is politics by other means..." methodological track. That being said, as he promised, he focused much less on battles than the social impact on the homefront, for instance. Miller is also on target in that we did investigate one of the very topics that he mentions as being a favorite: Hiroshima. The course was very well done and enjoyable and I learned a lot. But it was definitely presented from the perspective of social and diplomatic history, not military.

The Civil War course, on the other hand, was taught by a professor who was much more of a diplomatic/military historian. As such, he delved much deeper into tactics and battles, though he didn't neglect politics or diplomacy. He did, however, give relatively short shrift to social history. This course was also worthwhile, but, again, the dominant perspective was that of the discipline in which the professor specialized.

Thus, I believe that, when done properly, a general survey-type course--the kind most undergrads take--can effectively delve into tactics and battles as well as other areas (social, diplomatic, political). That's where I think Miller is a little off the mark. The traditional topics covered by military history are being taught as part of a larger, more comprehensive course that also covers history as studied via a wide variety of historical methodologies. That being said, he does make an important point.

Colleges and universities need to have military historians on campus who teach conventional military history courses as well as general surveys. First, and most in-line with Miller's critique, the continued popularity of books devoted to the military history of the Civil War and WWII show that there is a body of students out there who would be interested in straight forward military history courses. Thus, specific, upper level courses in military history would probably be well received and be attractive to many students.

Yet, to my mind, it is the role that military historians can play in the historical education of the broader student population that is more important. I saw many people interested in military history in my Civil War class. They were there for the guns and ended up learning about a whole lot more (yes, like about the "butter"). Similarly, there were people in my WWII class who were interested in the home front and Hiroshima, but also took away some knowledge about battles and a few tactics and how specific military capabilities and outcomes play a part in history.

What I'm getting at is that a military historian--just like a social or economic or diplomatic historian--brings a certain point of view to courses that deal with broader topics. It would be a shame if these perspectives are lost because they aren't popular enough amongst the academics or "sexy" enough for academic journals. The current impression is that any young historian simply can't make much headway with a specialization in military history. If there is no demand for this methodolgy, the supply will soon dry up and our understanding of war will be the worse for it.

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Sunday, 14 December 2014

50,000 mark!

I have for you one of life's great ponderous questions. Somewhat rhetorical, somewhat thought-provoking, somewhat unanswerable. It's a real head-scratcher. Ready to hear it?

Do you want the good news or the bad news first?

You don't actually get a choice because I'm going to tell you the good news first, I've just heard that opening with a question is a good way to hook readers in. Hopefully you're still reading...

Well the good news is that I completed NaNoWriMo (and succeeded in writing 50,000 words in the month of November). This was a feat that I really didn't think I could achieve so I was pleasantly surprised that I was able to make it, even if writing the last 5,000 words was more painful than when I jammed a paper clip underneath my fingernail last week in work... The point is, I did it! I got my word count to a point above 50,000, something that I believed I could never, ever, ever do.

But unfortunately the laws of physics relate to writing too (surprisingly enough) and we all know that what goes up must come down, for every action there is an equal and opposite reaction... Essentially, I discovered that making huge progress with my wordcount doesn't automatically equate to simultaneous progress with my plot line and character development.

What I mean is that I thought that by the time I reached 50,000 words I would have been a lot further along with my storyline. I always estimated (very naively, I now understand) that my novel would be approximately 80-90,000 words when I finished it. Therefore it makes sense that by the time I reached 50K words, I assumed that I would have been over the halfway point. But I'm not. I'm not even close to halfway. In fact, there are large parts of my novel that I left out in my haste to reach 50K. This means that I will have to go back and rewrite what I already have written, add in more chapters thus bumping up my wordcount even further and pushing me even further away from my ending!

Do I sound like I'm catastrophising? Sorry I tend do that, which in turn doesn't help with my writing. When I get stressed, confused or worried I tend to put my head in the sand and this is particularly true when it comes to writing. Why do you think it took me almost six years to sit down and finally make a decent attempt at writing my book?

So while I finished NaNo, made it to 50K and felt suitably smug for about a weekend, I then did what I do best: I panicked at the realisation that writing the book is turning out to be a lot harder than I thought (who'd have thought it?) and I avoided my novel. In fact, I've pretty much avoided it ever since.

But I've pulled my head out of the sand this weekend, even if it did take a few weeks, and I've managed to start writing again. Knowing that I have written 50,000 words means that I can do it again and make it to 100,000. And who knows, maybe I'll have to write another 50,000 after that before I get to write those two incredible words "The End", but I can do it. My book could be 300,000 words long when I finish the first draft (although I hope it won't be) but that's what first drafts are for. They're there to edit, revise and hone down until the finest part of the story is left.

So I may not have finished my book during NaNo but I'm so much further than I ever thought I would be!


Pork organisation urges clearer ‘slap marks’

AHDB Pork has provided instructions on how pig producers can achieve clear and legible ‘slap marks’ on its website to help improve traceability in the food chain.

Mick Sloyan, director of AHDB Pork, explained the importance of slap markings on pigs.

“We pride ourselves in this country on our traceability system that provides reassurance to customers here and in export markets. We have a world-leading real-time internet-based system for licencing the movement of pigs.

However, we still rely on the use of effective slap marking to identify individual pigs.”

He added: “We are allowed to use slap marks rather than ear tags because we have demonstrated that this works. In order to maintain this derogation we need to continue to ensure that slap marks are applied correctly and that they are legible before and after slaughter.”

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How to Break Through a Weight Loss Plateau

So, you’ve gone on a diet, things have been going well, and the weight has been coming off in a nice, steady fashion. Then, it happens. Suddenly, the numbers on the scale won’t budge. What’s happened?

You’ve hit a weight loss plateau? As disheartening as this can be, especially after all of your hard work, it is important to understand that hitting a weight loss plateau is actually quite normal. Regardless of how diligent you might be in following a good regimen, from time to time, you will experience a plateau. The important thing is to understand that this is normal and not give up. There are some steps you can take to get back on track and begin losing weight once again.

When most people experience a weight loss plateau, they are tempted to severely slash their calories in an effort to begin losing weight again. This is actually one of the worst things you can do. Instead, try the following techniques to begin dropping the weight again.

Weight Loss Plateau

Before we begin it’s also important to understand that the scale is usually wrong and not very accurate. If you see the scale isn’t moving downward a little bit each day this is quite normal. The body holds onto water and this can cause the scale to stay the same or even go up a little. In my personal opinion if you don’t see the scale move within a period of two weeks then you hit a plateau.

Adjust Your Caloric Intake

Go ahead and adjust your caloric intake, but take care not to restrict the calories too much. If you have noticed that you’re no longer losing weight, try simply cutting between 100 and 200 calories from your diet to begin making progress once again.

cutting calories

Please keep in mind it’s normal to not see any weight loss for a few days sometime on the scale. The body can hold a good bit of water which alters the number of the scale. You very well could be losing weight, but due to the water the scale numbers aren’t moving. In time the water does come off on it’s own.

Consider the Quality of Food You Are Eating

What types of food are you consuming? Are you relying heavily on processed foods? If so, make the switch to more quality whole foods, such as beans, vegetables, lean proteins, and high-fiber fruits, all of which can provide the energy your body needs to burn body fat.

And another reason you might not be losing any weight is because you’re consuming too many calories daily. If you’re counting calories it’s critical that you measure and weight your food with a kitchen scale. If not, you could be taking in an extra 200 – 400 calories a day which is keeping that scale from moving down.

Another problem you might not see the scale drop is because you’re eating out at restaurants too much.  Most popular restaurants under estimate the real amount of calories present in a dish. Especially the low calorie menu options. One example is the Zuppa Toscana soup from Olive Garden. I love this stuff and I order it every time I go, but the calories aren’t accurate in most cases.

stop eating out to lose weight

According to the website Live Science, research has been done that shows this soup which is supposed to contain 191 calories actually measured closer to 391 calories. I’ll link to the article here as it’s an interesting read. You can eat out at restaurants and enjoy yourself but remember that the calories might not be 100% accurate. You might find that the reason you haven’t been losing is you’re just consuming too many calories.

Switch Up Your Routine

Have you been following the same workout routine for the past several weeks or even months? If so, it could be time to change things up a bit. As your muscles become familiar with the same exercise routine, it tends to become less effective. To produce a change in your body fat loss, it’s necessary to step outside your comfort zone.

Try including some high intensity interval training, which has been shown to be incredibly effective at burning body fat. This could be done by alternating walking and running, during a boot camp class, or even speed walking. Work on progressing slowly when including high-intensity exercise into your normal workout routine.

If you attempt to include this type of exercise too fast, you will likely end up feeling tired and sore and could even be at risk for an injury. And always check with your doctors first to make sure it’s okay.

Get Enough Sleep

Seems simple right? Are you getting a sufficient amount of sleep? If not, your body could actually be holding onto weight. A full night of sleep is essential to losing body fat because it allows your body to reset your hormones naturally.

Sleep is great for fat loss

While it might not seem like much, even slight sleep deprivation could result in increased levels of cortisol, which is a stress hormone. That can lead to an accumulation of body fat, especially around the midsection. So, if you have been burning the candle at both ends, make an effort to get eight full hours of sleep each night.

Use Fluids to Flush Your Body

Did you know that your body can crave food when you are even slightly dehydrated? It’s true. Many times, when you think you are hungry, you are actually thirsty. If your body is not getting enough fluids, you could fall into the trap of eating more than you realize, which could lead to a weight loss plateau or even weight gain. Make sure you are drinking enough fluids to flush her body each day and prevent overeating…

And I know you’ll thinking if the body holds onto water then won’t drinking more keep the fat from coming off based on what I said earlier? Nope, not at all my friend. Water weight is not the same as losing fat. Two different things.

You’re body could hold on to 2 to 3 pounds of water in some cases, but you could still be losing fat. So don’t worry. Drinking enough water is critical to losing weight and will help keep you full.

Eat More Protein

As contradictory as it might seem, eating more protein can actually help you to boost a weight loss plateau. Of all of the various types of food, protein has the highest thermic effect. This means it is capable of burning more calories during the digestion process.

Protein for fat loss

Additionally, protein also contains leucine, which is an amino acid. Research shows that this amino acid serves as a powerful catalyst for burning fat.

Protein is also essential in keeping your body from losing too much muscle which tends to happen sometimes when people lose weight. A good serving of protein will also help keep you nice and full which helps with cravings and feelings of hunger. If you have trouble adding in enough protein into your diet I recommend a quality protein powder. The one I use and recommend is Biotrust Low Carb. You can even use protein powder in different recipes too.

Be Careful with Caffeine

Are you a fan of coffee, energy drinks or other caffeinated beverages? If so, your coffee habit could be making an impact on your weight loss plans. According to research, if you drink more than five cups of coffee daily, you could experience problems with increased belly fat storage.

How to Break Through a Weight Loss Plateau

Conversely, a separate study found that combining five cups of green tea with three hours of exercise weekly could help you lose two more pounds than if you don’t drink tea.

Why exactly is green tea so helpful for losing weight? It’s the compounds known as catechins contained in green tea that help to whittle away belly fat by giving your metabolism a boost. If you find that you just can’t give up your caffeine habit, but you have hit a weight loss plateau, consider making the switch to green tea to get back on track.

Consider “Cheating” on Your Diet

In most cases, it simply is not a good idea to cheat on your diet, but if you are having trouble breaking past a plateau, indulging in an additional 600-700 calorie “cheat meal” also known in some circles as a refeed could be just what you need to get your weight loss moving in the right direction again. Let me explain…

In order to gain the most benefits from this technique; however, you need to make sure you eat the right foods as part of your cheat meal. This means a meal rich in carbs. Within a few days, you should start seeing weight loss progress once again.

Wondering why this works? It’s because when you lose weight, you also lose fat. the less fat your body has, the less leptin you produce. Leptin is known as the satiety hormone and it is responsible for telling your brain to conserve calories in order to prevent your body from starving.

According to research, the best way to increase your body’s leptin production is to consume more carbohydrates. Unlike protein and fat, carbs transmit messages to your brain that you are not starving and convince your body to burn calories at a more normal rate rather than holding onto them.

Eating hamburger, donuts, a little ice cream or a slice of pizza could be just what you need to trick your body into boosting your caloric burn, giving you the weight loss you want. Here’s an example of what I do each week with my refeed.

Refeed day

Each week usually on Friday or Saturday I consume an extra 600 to 700 calories in mostly carbs. I typical eat 2,000 calories a day (a calorie deficit) and I’m a big believer in counting them. So on Friday or Saturday I would add an additional 600-700 calories in mostly carbs.

You may see a slight gain on the scale the next day, but that’s just due to increased water intake because you increased the carbs. Don’t worry about that at all. It will come off. Doing this once a week will help you keep you burning fat. I prefer this more than a cheat day because it’s very easy to over eat during the course of the entire day. A refeed day is planned and organized and helps keep you from over eating.

Take a Much Needed “Maintenance” Break

I know this may seem crazy, but when you hit a plateau sometimes the best way to overcome it is by taking a short break. When you’re dieting and eating a calorie deficit for a period of time you’re body start’s to see a decline in certain hormones. I touched on this earlier in the tip above this one. Doing the refeeds helps to prevent this, but after about 4 months of dieting I recommend you take a 2 week break.

During this 2 week break you can start eating at “maintenance” which gives your body a chance to recoup and recover. Eating at maintenance means you’re eating enough calories to not lose weight and not gain weight. You’ll eating just enough to maintain your current weight. There are a number of different online calculators to help you figure out how many calories you need to eat for maintenance.

It may seem crazy, but this will send a signal to your body that you’re okay and not starving. It can also serve as a nice mental boost for you. Eat whatever during this time, but just make sure you eat the correct amount of calories for maintenance.

Eating at Maintenance

After the two weeks is up you can then start dieting again and you should see you’ve broken through the weight loss plateau. Now, you will notice the scale jumping up in weight. This is completely normal and don’t worry. During maintenance you’ll consuming a lot more calories than you were when dieting which means more water weight.

If you’re correctly eating at maintenance you won’t gain any fat and any weight gain you see on the scale will just be water weight. So completing this two week “maintenance” and then going right back to your diet should help to kick start fat burning again. I recommend only doing a maintenance after 4 months of dieting aka being in a calorie deficit.

In the end, going through a plateau is a normal part of losing weight. It happens to pretty much everyone at some point and time. We all want to see progress as fast as possible, but remember a plateau is normal and just the body’s way of making sure you’re okay. It’s the body taking notice and saying “Hey, I’ve noticed you’ve been losing some weight lately. I’m just going to hold off for a few and keep you at this weight to make sure everything is okay”.

Just stay focused and don’t lose your motivation. You’ll start losing weight again eventually and hopefully these tips will help you break through your next weight loss plateau.


August 5, 6:30PM - August 6, 9:00AM

Join Zoo Boise for an overnight adventure. Families will experience a campout unlike any other. Sleep under the stars right in the middle of the city. Enjoy programs led by education department staff or explore the zoo on your own after regular zoo hours. The event goes from 6:30 p.m. Aug. 5 to 9 a.m. Aug. 6.


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Description: Located in the heart of Davie,this beautiful, strategically located, unfurnished apartment, features 3 bedrooms, 2 bathrooms and new kitchen appliances. It is part of a community that offers a private gym, game room, tennis and volleyball court. The unit is 5 minutes walking distance from NOVA university and just few minutes away from Broward College and other main educational institutions. Addittionally, it offers a very diverse restaurant and shopping access in a safe neighborhood.

Calculate your interest rates and payment plan now!
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logo multiInstanceLearning

A collection of multi-instance learning classifiers. Includes the Citation KNN method, several variants of the diverse density method, support vector machines for multi-instance learning, simple wrappers for applying standard propositional learners to multi-instance data, decision tree and rule learners, and some other methods.

homepage: weka.sourceforge.net/doc.packages/multiInstanceLearning
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packaging: jar
get this artifact from: central
see this artifact on: search.maven.org

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Claude Debussy: Clair De Lune (Organ)

Books | Organ

Catalogue No: EA13048
Composer: Claude Debussy
Format: Sheet Music | Instrumental Album
Debussy’s beautiful, beloved Clair De Lune was written as the third movement of his Suite Bergamasque at the turn of the last century. It was inspired by a poem of contemporary Paul Verlaine and is a significant example of Debussy’s innovative use of key, time and tonal colour. The piece has been arranged for Orchestra, though not by Debussy, Harp, Guitar and many other instrumental combinations. Clair De Lune was composed for Piano in D flat and has here been transposed to C.
Skill Level: Advanced Explain this
No of pages: 8
Language: English
Publisher: Edwin Ashdown

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Csir syllabus paper 2011

  1. 1. www.helpBIOTECH.blogspot.com | Your Gate Way to the Life Science Career CSIR-UGC National Eligibility Test (NET) for Junior Research Fellowship and Lecturer-ship SYLLABUS FOR LIFE SCIENCES PAPER I AND PAPER II1. MOLECULES AND THEIR INTERACTION RELAVENT TO BIOLOGY A. Structure of atoms, molecules and chemical bonds. B. Composition, structure and function of biomolecules (carbohydrates, lipids, proteins, nucleic acids and vitamins). C. Stablizing interactions (Van der Waals, electrostatic, hydrogen bonding, hydrophobic interaction, etc.). D. Principles of biophysical chemistry (pH, buffer, reaction kinetics, thermodynamics, colligative properties). E. Bioenergetics, glycolysis, oxidative phosphorylation, coupled reaction, group transfer, biological energy transducers. F. Principles of catalysis, enzymes and enzyme kinetics, enzyme regulation, mechanism of enzyme catalysis, isozymes. G. Conformation of proteins (Ramachandran plot, secondary, tertiary and quaternary structure; domains; motif and folds). H. Conformation of nucleic acids (A-, B-, Z-,DNA), t-RNA, micro-RNA). I. Stability of protein and nucleic acid structures. J. Metabolism of carbohydrates, lipids, amino acids, nucleotides and vitamins.2. CELLULAR ORGANIZATIONA. Membrane structure and function: Structure of model membrane, lipid bilayer and membrane protein diffusion, osmosis, ion channels, active transport, ion pumps, mechanism of sorting and regulation of intracellular transport, electrical properties of membranes.B. Structural organization and function of intracellular organelles: Cell wall, nucleus, mitochondria, Golgi bodies, lysosomes, endoplasmic reticulum, peroxisomes, plastids, vacuoles, chloroplast, structure & function of cytoskeleton and its role in motility.C. Organization of genes and chromosomes: Operon, interrupted genes, gene families, structure of chromatin and chromosomes, unique and repetitive DNA, heterochromatin, euchromatin, transposons.D. Cell division and cell cycle: Mitosis and meiosis, their regulation, steps in cell cycle, and control of cell cycle.E. Microbial Physiology: Growth, yield and characteristics, strategies of cell division, stress response.
  2. 2. www.helpBIOTECH.blogspot.com | Your Gate Way to the Life Science Career3. FUNDAMENTAL PROCESSESA. DNA replication, repair and recombination: Unit of replication, enzymes involved, replication origin and replication fork, fidelity of replication, extrachromosomal replicons, DNA damage and repair mechanisms.B. RNA synthesis and processing: Transcription factors and machinery, formation of initiation complex, transcription activators and repressors, RNA polymerases, capping, elongation and termination, RNA processing, RNA editing, splicing, polyadenylation, structure and function of different types of RNA, RNA transport.C. Protein synthesis and processing: Ribosome, formation of initiation complex, initiation factors and their regulation, elongation and elongation factors, termination, genetic code, aminoacylation of tRNA, tRNA-identity, aminoacyl tRNA synthetase, translational proof-reading, translational inhibitors, post- translational modification of proteins.D. Control of gene expression at transcription and translation level: Regulation of phages, viruses, prokaryotic and eukaryotic gene expression, role of chromatin in regulating gene expression and gene silencing.4. CELL COMMUNICATION AND CELL SIGNALINGA. Host parasite interaction: Recognition and entry processes of different pathogens like bacteria, viruses into animal and plant host cells, alteration of host cell behavior by pathogens, virus-induced cell transformation, pathogen-induced diseases in animals and plants, cell-cell fusion in both normal and abnormal cells.B. Cell signaling: Hormones and their receptors, cell surface receptor, signaling through G-protein coupled receptors, signal transduction pathways, second messengers, regulation of signaling pathways, bacterial and plant two-component signaling systems, bacterial chemotaxis and quorum sensing.C. Cellular communication: Regulation of hematopoiesis, general principles of cell communication, cell adhesion and roles of different adhesion molecules, gap junctions, extracellular matrix, integrins, neurotransmission and its regulation.D. Cancer: Genetic rearrangements in progenitor cells, oncogenes, tumor suppressor genes, cancer and the cell cycle, virus-induced cancer, metastasis, interaction of cancer cells with normal cells, apoptosis, therapeutic interventions of uncontrolled cell growth.
  3. 3. www.helpBIOTECH.blogspot.com | Your Gate Way to the Life Science CareerE. Innate and adaptive immune system: Cells and molecules involved in innate and adaptive immunity, antigens, antigenicity and immunogenicity. B and T cell epitopes, structure and function of antibody molecules, generation of antibody diversity, monoclonal antibodies, antibody engineering, antigen-antibody interactions, MHC molecules, antigen processing and presentation, activation and differentiation of B and T cells, B and T cell receptors, humoral and cell- mediated immune responses, primary and secondary immune modulation, the complement system, Toll-like receptors, cell-mediated effector functions, inflammation, hypersensitivity and autoimmunity, immune response during bacterial (tuberculosis), parasitic (malaria) and viral (HIV) infections, congenital and acquired immunodeficiencies, vaccines.5. DEVELOPMENTAL BIOLOGYA. Basic concepts of development: Potency, commitment, specification, induction, competence, determination and differentiation; morphogenetic gradients; cell fate and cell lineages; stem cells; genomic equivalence and the cytoplasmic determinants; imprinting; mutants and transgenics in analysis of development.B. Gametogenesis, fertilization and early development: Production of gametes, cell surface molecules in sperm-egg recognition in animals; embryo sac development and double fertilization in plants; zygote formation, cleavage, blastula formation, embryonic fields, gastrulation and formation of germ layers in animals; embryogenesis, establishment of symmetry in plants; seed formation and germination.C. Morphogenesis and organogenesis in animals: Cell aggregation and differentiation in Dictyostelium; axes and pattern formation in Drosophila, amphibia and chick; organogenesis – vulva formation in Caenorhabditis elegans; eye lens induction, limb development and regeneration in vertebrates; differentiation of neurons, post embryonic development-larval formation, metamorphosis; environmental regulation of normal development; sex determination.D. Morphogenesis and organogenesis in plants: Organization of shoot and root apical meristem; shoot and root development; leaf development and phyllotaxy; transition to flowering, floral meristems and floral development in Arabidopsis and Antirrhinum.E. Programmed cell death, aging and senescence.
  4. 4. www.helpBIOTECH.blogspot.com | Your Gate Way to the Life Science Career6. SYSTEM PHYSIOLOGY - PLANTA. Photosynthesis: Light harvesting complexes; mechanisms of electron transport; photoprotective mechanisms; CO2 fixation-C3, C4 and CAM pathways.B. Respiration and photorespiration: Citric acid cycle; plant mitochondrial electron transport and ATP synthesis; alternate oxidase; photorespiratory pathway.C. Nitrogen metabolism: Nitrate and ammonium assimilation; amino acid biosynthesis.D. Plant hormones: Biosynthesis, storage, breakdown and transport; physiological effects and mechanisms of action.E. Sensory photobiology: Structure, function and mechanisms of action of phytochromes, cryptochromes and phototropins; stomatal movement; photoperiodism and biological clocks.F. Solute transport and photoassimilate translocation: Uptake, transport and translocation of water, ions, solutes and macromolecules from soil, through cells, across membranes, through xylem and phloem; transpiration; mechanisms of loading and unloading of photoassimilates.G. Secondary metabolites - Biosynthesis of terpenes, phenols and nitrogenous compounds and their roles.H. Stress physiology: Responses of plants to biotic (pathogen and insects) and abiotic (water, temperature and salt) stresses; mechanisms of resistance to biotic stress and tolerance to abiotic stress7. SYSTEM PHYSIOLOGY - ANIMALA. Blood and circulation: Blood corpuscles, haemopoiesis and formed elements, plasma function, blood volume, blood volume regulation, blood groups, haemoglobin, immunity, haemostasis.B. Cardiovascular System: Comparative anatomy of heart structure, myogenic heart, specialized tissue, ECG – its principle and significance, cardiac cycle, heart as a pump, blood pressure, neural and chemical regulation of all above.C. Respiratory system: Comparison of respiration in different species, anatomical considerations, transport of gases, exchange of gases, waste elimination, neural and chemical regulation of respiration.
  5. 5. www.helpBIOTECH.blogspot.com | Your Gate Way to the Life Science CareerD. Nervous system: Neurons, action potential, gross neuroanatomy of the brain and spinal cord, central and peripheral nervous system, neural control of muscle tone and posture.E. Sense organs: Vision, hearing and tactile response.F. Excretory system: Comparative physiology of excretion, kidney, urine formation, urine concentration, waste elimination, micturition, regulation of water balance, blood volume, blood pressure, electrolyte balance, acid-base balance.G. Thermoregulation: Comfort zone, body temperature – physical, chemical, neural regulation, acclimatization.H. Stress and adaptationI. Digestive system: Digestion, absorption, energy balance, BMR.J. Endocrinology and reproduction: Endocrine glands, basic mechanism of hormone action, hormones and diseases; reproductive processes, neuroendocrine regulation.8. INHERITANCE BIOLOGYA. Mendelian principles: Dominance, segregation, independent assortment, deviation from Mendelian inheritance.B. Concept of gene: Allele, multiple alleles, pseudoallele, complementation tests.C. Extensions of Mendelian principles: Codominance, incomplete dominance, gene interactions, pleiotropy, genomic imprinting, penetrance and expressivity, phenocopy, linkage and crossing over, sex linkage, sex limited and sex influenced characters.D. Gene mapping methods: Linkage maps, tetrad analysis, mapping with molecular markers, mapping by using somatic cell hybrids, development of mapping population in plants.E. Extra chromosomal inheritance: Inheritance of mitochondrial and chloroplast genes, maternal inheritance.F. Microbial genetics: Methods of genetic transfers – transformation, conjugation, transduction and sex-duction, mapping genes by interrupted mating, fine structure analysis of genes.G. Human genetics: Pedigree analysis, lod score for linkage testing, karyotypes, genetic disorders.
  6. 6. www.helpBIOTECH.blogspot.com | Your Gate Way to the Life Science CareerH. Quantitative genetics: Polygenic inheritance, heritability and its measurements, QTL mapping.I. Mutation: Types, causes and detection, mutant types – lethal, conditional, biochemical, loss of function, gain of function, germinal verses somatic mutants, insertional mutagenesis.J. Structural and numerical alterations of chromosomes: Deletion, duplication, inversion, translocation, ploidy and their genetic implications.K. Recombination: Homologous and non-homologous recombination, including transposition, site-specific recombination.9. DIVERSITY OF LIFE FORMSA. Principles and methods of taxonomy:Concepts of species and hierarchical taxa, biological nomenclature, classical and quantititative methods of taxonomy of plants, animals and microorganisms.B. Levels of structural organization: Unicellular, colonial and multicellular forms; levels of organization of tissues, organs and systems; comparative anatomy.C. Outline classification of plants, animals and microorganisms:Important criteria used for classification in each taxon; classification of plants, animals and microorganisms; evolutionary relationships among taxa.D. Natural history of Indian subcontinent: Major habitat types of the subcontinent, geographic origins and migrations of species; common Indian mammals, birds; seasonality and phenology of the subcontinent.E. Organisms of health and agricultural importance: Common parasites and pathogens of humans, domestic animals and crops.10. ECOLOGICAL PRINCIPLES A. The Environment: Physical environment; biotic environment; biotic and abiotic interactions. B. Habitat and niche: Concept of habitat and niche; niche width and overlap; fundamental and realized niche; resource partitioning; character displacement.
  7. 7. www.helpBIOTECH.blogspot.com | Your Gate Way to the Life Science CareerC. Population ecology: Characteristics of a population; population growth curves; population regulation; life history strategies (r and K selection); concept of metapopulation – demes and dispersal, interdemic extinctions, age structured populations.D. Species interactions: Types of interactions, interspecific competition, herbivory, carnivory, pollination, symbiosis.E. Community ecology: Nature of communities; community structure and attributes; levels of species diversity and its measurement; edges and ecotones.F. Ecological succession: Types; mechanisms; changes involved in succession; concept of climax.G. Ecosystem: Structure and function; energy flow and mineral cycling (CNP); primary production and decomposition; structure and function of some Indian ecosystems: terrestrial (forest, grassland) and aquatic (fresh water, marine, eustarine).H. Biogeography: Major terrestrial biomes; theory of island biogeography; biogeographical zones of India.I. Applied ecology: Environmental pollution; global environmental change; biodiversity-status, monitoring and documentation; major drivers of biodiversity change; biodiversity management approaches.J. Conservation biology: Principles of conservation, major approaches to management, Indian case studies on conservation/management strategy (Project Tiger, Biosphere reserves).11. EVOLUTION AND BEHAVIOURA. Emergence of evolutionary thoughts: Lamarck; Darwin–concepts of variation, adaptation, struggle, fitness and natural selection; Mendelism; spontaneity of mutations; the evolutionary synthesis.B. Origin of cells and unicellular evolution: Origin of basic biological molecules; abiotic synthesis of organic monomers and polymers; concept of Oparin and Haldane; experiment of Miller (1953); the first cell; evolution of prokaryotes; origin of eukaryotic cells; evolution of unicellular eukaryotes; anaerobic metabolism, photosynthesis and aerobic metabolism.C. Paleontology and evolutionary history: The evolutionary time scale; eras, periods and epoch; major events in the evolutionary time scale; origins of unicellular and multicellular organisms; major groups of plants and animals; stages in primate evolution including Homo.
  8. 8. www.helpBIOTECH.blogspot.com | Your Gate Way to the Life Science CareerD. Molecular Evolution: Concepts of neutral evolution, molecular divergence and molecular clocks; molecular tools in phylogeny, classification and identification; protein and nucleotide sequence analysis; origin of new genes and proteins; gene duplication and divergence.E. The Mechanisms: Population genetics – populations, gene pool, gene frequency; Hardy-Weinberg law; concepts and rate of change in gene frequency through natural selection, migration and random genetic drift; adaptive radiation and modifications; isolating mechanisms; speciation; allopatricity and sympatricity; convergent evolution; sexual selection; co-evolution.F. Brain, Behavior and Evolution: Approaches and methods in study of behavior; proximate and ultimate causation; altruism and evolution-group selection, kin selection, reciprocal altruism; neural basis of learning, memory, cognition, sleep and arousal; biological clocks; development of behavior; social communication; social dominance; use of space and territoriality; mating systems, parental investment and reproductive success; parental care; aggressive behavior; habitat selection and optimality in foraging; migration, orientation and navigation; domestication and behavioral changes.12. APPLIED BIOLOGY: A. Microbial fermentation and production of small and macro molecules. B. Application of immunological principles (vaccines, diagnostics). tissue and cell culture methods for plants and animals. C. Transgenic animals and plants, molecular approaches to diagnosis and strain identification. D. Genomics and its application to health and agriculture, including gene therapy. E. Bioresource and uses of biodiversity. F. Breeding in plants and animals, including marker – assisted selection. G. Bioremediation and phytoremediation. H. Biosensors.
  9. 9. www.helpBIOTECH.blogspot.com | Your Gate Way to the Life Science Career13. METHODS IN BIOLOGYA. Molecular biology and recombinant DNA methods: Isolation and purification of RNA , DNA (genomic and plasmid) and proteins, different separation methods; analysis of RNA, DNA and proteins by one and two dimensional gel electrophoresis, isoelectric focusing gels; molecular cloning of DNA or RNA fragments in bacterial and eukaryotic systems; expression of recombinant proteins using bacterial, animal and plant vectors; isolation of specific nucleic acid sequences; generation of genomic and cDNA libraries in plasmid, phage, cosmid, BAC and YAC vectors; in vitro mutagenesis and deletion techniques, gene knock out in bacterial and eukaryotic organisms; protein sequencing methods, detection of post-translation modification of proteins; DNA sequencing methods, strategies for genome sequencing; methods for analysis of gene expression at RNA and protein level, large scale expression analysis, such as micro array based techniques; isolation, separation and analysis of carbohydrate and lipid molecules; RFLP, RAPD and AFLP techniquesB. Histochemical and immunotechniques: Antibody generation, detection of molecules using ELISA, RIA, western blot, immunoprecipitation, floweytometry and immunofluorescence microscopy, detection of molecules in living cells, in situ localization by techniques such as FISH and GISH.C. Biophysical methods: Analysis of biomolecules using UV/visible, fluorescence, circular dichroism, NMR and ESR spectroscopy, structure determination using X-ray diffraction and NMR; analysis using light scattering, different types of mass spectrometry and surface plasma resonance methods.D. Statistical Methods: Measures of central tendency and dispersal; probability distributions (Binomial, Poisson and normal); sampling distribution; difference between parametric and non-parametric statistics; confidence interval; errors; levels of significance; regression and correlation; t-test; analysis of variance; X2 test;; basic introduction to Muetrovariate statistics, etc.E. Radiolabeling techniques: Properties of different types of radioisotopes normally used in biology, their detection and measurement; incorporation of radioisotopes in biological tissues and cells, molecular imaging of radioactive material, safety guidelines.F. Microscopic techniques: Visulization of cells and subcellular components by light microscopy, resolving powers of different microscopes, microscopy of living cells, scanning and transmission microscopes, different fixation and staining techniques for EM, freeze-etch and freeze-fracture methods for EM, image processing methods in microscopy.G. Electrophysiological methods: Single neuron recording, patch-clamp recording, ECG, Brain activity recording, lesion and stimulation of brain, pharmacological testing, PET, MRI, fMRI, CAT .
  10. 10. www.helpBIOTECH.blogspot.com | Your Gate Way to the Life Science CareerH. Methods in field biology: Methods of estimating population density of animals and plants, ranging patterns through direct, indirect and remote observations, sampling methods in the study of behavior, habitat characterization-ground and remote sensing methods.I. Computational methods: Nucleic acid and protein sequence databases; data mining methods for sequence analysis, web-based tools for sequence searches, motif analysis and presentation.


Computer Science

Introduction to Computer Systems

Introduction to Computer Systems
How a computer works, from hardware to high-level programming. Logic circuits, computer instructions, assembly language, binary arithmetic, C programming, program translation, data structures, and algorithm analysis.
 Hours3.0 Credit, 3.0 Lecture, 2.0 Lab
 PrerequisitesC S 142; or instructor's consent.
 NoteStudents are allowed only 1 retake of C S 224. This includes students who have failed or withdrawn (received a "W" grade). If after 1 retake, a student needs to retake the course again, the student must wait 1 semester/term before being allowed to take any C S course and must follow the petition process at This policy does not apply to classes dropped before the add/drop deadline. Petitions for exceptions to the policy can be completed at
 TaughtFall, Winter, Spring even years, Summer odd years
 ProgramsContaining C S 224
Course Outcomes:

Binary Computations

Ability to perform simple computations in binary.

Translating C code to Assembly

Ability to describe how a compiler translates C code to assembly.

Boolean Logic

Perform computations using Boolean logic

Translate Boolean

Translate Boolean logic to transistor circuitry

Computer Operation

Ability to describe the operation of a computer at the micro-architectural level

Use combinational and sequential circuitry to implement an instruction set architecture

C Programming

Ability to program in C.

Assembly Programming

Ability to program in assembly.

Computer Architecture

Ability to describe the high level organization and operation of a computer, e.g. the von Neumann model


Saturday, August 23, 2014

Arguments Not Worth Having

Watching the “Ice Bucket Challenge” phenomenon become the hit social media trend of this summer, I have decided to start a new series on this blog: Arguments Not Worth Having.

Here are three right off the bat:

1. Goofy disability awareness or fundraising campaigns.

2. The unbeatable popularity of fundraising for cures.

3. Language that likens disability to war or a fistfight.

I haven’t fully worked out the criteria for determining which arguments I believe are not worth having, but they involve some combination of the following factors:

- The thing is something disability-related that non-disabled people really like.

- A non-trivial number of disabled people seem to like it, too.

- The thing is something I don’t like, or I think it’s silly, or I feel uncomfortable with it, but it doesn’t really offend me.

- I could make a logical, consistent argument against the thing, but I would really have to work at it, and the argument would have at least two or three distinct layers to get through.

- The likelihood that anyone will be convinced or even understand my thinking on the thing is below 20%.

- There is a 90% possibility that at the end of the argument, I will sound like an over-educated, unemotional robot with no human feelings or sense of humor.

- The thing is stupid, but not harmful. The consequences of leaving the thing alone are low.

No comments:


Mathematics for biologists 1989/90, 1990/91, 1992/93.

For 1st year biology students. Average program.
Official name: Istituzioni di Matematiche per biologi.

ELEMENTARY METHODS What is mathematics? Fundamental rules The logarithm Trigonometric functions Polar coordinates in plane and space Complex numbers n-th roots of complex numbers The language of set theory Peano's axioms and the principle of induction Some logic Operations on sets with infinitely many operandss The cartesian product Resolution of systems of linear equations with Gauss elimination Binomial numbers Euclidean algorithm FUNCTIONS AND RELATIONS Functions Relations Equivalence relations REAL NUMBERS sqrt(2) is irrational Real numbers SEQUENCES AND SERIES Sequences of real numbers Sequences tending to infinity The Bolzano-Weierstrass theorem Convergence criteria for sequences Limsup and liminf Sequences of complex numbers Numerical series Convergence criteria specific for series ANALYTIC GEOMETRY Linear subspaces of R^n Linear independence, bases and dimension Affine subspaces of R^n The scalar product Linear mappings and matrices Determinants and vector product CONTINUOUS FUNCTIONS Triangular inequality in R^n Limit of f(x) for x tending to x_0 Continuous functions defined on a subset of R^m Polynomial functions The existence of zeros for continuous functions Existence of the maximum of a continuous function defined on a compact set Pointwise and uniform convergence of sequences of functions Logarithms (theory) DIFFERENTIAL CALCULUS IN ONE VARIABLE The equation y = y_0+a(x-x_0) The derivative The derivatives of trigonometric functions The derivative of the exponential and the logarithm Relative maxima and minima and Rolle's theorem The marvelous theorem of calculus Analytic study of the graph of a function Taylor series of a polynomial Taylor series of a differentiable function De l'Hopital's rules Inversion of trigonometric functions INTEGRATION Measures Measurable sets and Caratheodory's theorem Measurable functions The integral Fundamental inequality of integration theory Lebesgue measure Fundamental theorem of calculus Calculating integrals by means of the fundamental theorem Integration by parts Transformation rules for the integral


Monday, July 31, 2017

Robots taking our jobs

The figures below are from the recent paper Robots and Jobs: Evidence from US Labor Markets, by Acemoglu and Restrepo.

VoxEU discussion:
... Estimates suggest that an extra robot per 1000 workers reduces the employment to population ratio by 0.18-0.34 percentage points and wages by 0.25-0.5%. This effect is distinct from the impacts of imports, the decline of routine jobs, offshoring, other types of IT capital, or the total capital stock.
If the robot does the work of a few workers, that explains the fraction of a percent (negative) effect on employment and compensation in a model with direct substitution of robot labor for human work, and smaller second order (positive) effect from comparative advantage of humans in complementary jobs. This is not the optimistic scenario where buggy whip makers displaced by the automobile easily find good new jobs in the expanded economy. We can expect to see many more robots (and virtual AI robots) per 1000 workers in the near future.

Related talk at HKUST by Harvard labor economist Richard Freeman: Work and Income in the Age of Robots and AI. This time it's different?

Here's Richard in 2011 when we were working on a project at Alibaba headquarters :-)

China's rise in Science and Engineering indicators (NSF)

Data from the 2016 NSF report on global Science & Engineering Indicators shows the rapid rise of China in both academic science and applied technology.

Rapid growth in number of Chinese S&E articles, reaching parity with US in 2013, and well ahead of Japan and India.

Fraction of high impact (top 1% most cited) papers highest for US research (~1.9%). China and Japan comparable at ~0.8% as of 2012. China's fraction roughly doubled between 2001 and 2012.

As of today total number of high impact papers is still probably ~2:1 in favor of US. But I think most people would be surprised to see that China has caught up with (surpassed?) Japan in this quality metric.

US and China now each account for ~30% of global high tech value-added manufacturing. Value-added means net of input components -- going beyond simple assembly.

Sunday, July 30, 2017

Like little monkeys: How the brain does face recognition

This is a Caltech TEDx talk from 2013, in which Doris Tsao discusses her work on the neuroscience of human face recognition. Recently I blogged about her breakthrough in identifying the face recognition algorithm used by monkey (and presumably human) brains. The algorithm seems similar to those used in machine face recognition: individual neurons perform feature detection just as in neural nets. This is not surprising from a purely information-theoretic perspective, if we just think about the space of facial variation and the optimal encoding. But it is amazing to be able to demonstrate it by monitoring specific neurons in a monkey brain.

An earlier research claim (which, four years ago, she recapitulates @8:50min in the video), that certain neurons are sensitive only to specific faces, seems not to be true. I always found it implausible.

On her faculty web page Tsao talks about her decision to attend Caltech as an undergraduate:
One day, my father went on a trip to California and took a tour of Caltech with a friend. He came back and told me about a monastery for science, located under the mountains amidst flowers and orange trees, where all the students looked very skinny and super smart, like little monkeys. I was intrigued. I went to a presentation about Caltech by a visiting admissions officer, who showed slides of students taking tests under olive trees, swimming in the Pacific, huddled in a dorm room working on a problem set... I decided: this is where I want to go to college! I dreamed every day about being accepted to Caltech. After I got my acceptance letter, I began to worry that I would fall behind in the first year, since I had heard about how hard the course load is. So I went to the library and started reading the Feynman Lectures. This was another world…where one could see beneath the surface of things, ask why, why, why, why? And the results of one’s mental deliberations actually could be tested by experiments and reveal completely unexpected yet real phenomena, like magnetism as a consequence of the invariance of the speed of light.
See also Feynman Lectures: Epilogue and Where Men are Men, and Giants Walk the Earth.

Thursday, July 27, 2017

First Human Embryos Edited in U.S. (MIT Technology Review)

It's only a matter of time... Note this kind of work can be done very secretly and with very modest resources -- it does not require banks of centrifuges, big reactors, or ICBM test launches.
First Human Embryos Edited in U.S. (MIT Technology Review)

Researchers have demonstrated they can efficiently improve the DNA of human embryos.

The U.S. intelligence community last year called CRISPR a potential "weapon of mass destruction.”

... Mitalipov and his colleagues are said to have convincingly shown that it is possible to avoid both mosaicism and “off-target” effects, as the CRISPR errors are known.

A person familiar with the research says “many tens” of human IVF embryos were created for the experiment using the donated sperm of men carrying inherited disease mutations.
Work on cognitive enhancement will probably be done first in monkeys, proving Planet of the Apes prophetic within the next decade or so :-)
His team’s move into embryo editing coincides with a report by the U.S. National Academy of Sciences in February that was widely seen as providing a green light for lab research on germline modification.

The report also offered qualified support for the use of CRISPR for making gene-edited babies, but only if it were deployed for the elimination of serious diseases.

The advisory committee drew a red line at genetic enhancements—like higher intelligence. “Genome editing to enhance traits or abilities beyond ordinary health raises concerns about whether the benefits can outweigh the risks, and about fairness if available only to some people,” said Alta Charo, co-chair of the NAS’s study committee and professor of law and bioethics at the University of Wisconsin–Madison.

Despite such barriers, the creation of a gene-edited person could be attempted at any moment, including by IVF clinics operating facilities in countries where there are no such legal restrictions.

Tuesday, July 25, 2017

Natural Selection and Body Shape in Eurasia

Prior to the modern era of genomics, it was claimed (without good evidence) that divergences between isolated human populations were almost entirely due to founder effects or genetic drift, and not due to differential selection caused by disparate local conditions. There is strong evidence now against this claim. Many of the differences between modern populations arose over relatively short timescales (e.g., ~10ky), due to natural selection.
Polygenic Adaptation has Impacted Multiple Anthropometric Traits

Jeremy J Berg, Xinjun Zhang, Graham Coop

Most of our understanding of the genetic basis of human adaptation is biased toward loci of large phenotypic effect. Genome wide association studies (GWAS) now enable the study of genetic adaptation in highly polygenic phenotypes. Here we test for polygenic adaptation among 187 world- wide human populations using polygenic scores constructed from GWAS of 34 complex traits. By comparing these polygenic scores to a null distribution under genetic drift, we identify strong signals of selection for a suite of anthropometric traits including height, infant head circumference (IHC), hip circumference (HIP) and waist-to-hip ratio (WHR), as well as type 2 diabetes (T2D). In addition to the known north-south gradient of polygenic height scores within Europe, we find that natural selection has contributed to a gradient of decreasing polygenic height scores from West to East across Eurasia, and that this gradient is consistent with selection on height in ancient populations who have contributed ancestry broadly across Eurasia. We find that the signal of selection on HIP can largely be explained as a correlated response to selection on height. However, our signals in IHC and WC/WHR cannot, suggesting a response to selection along multiple axes of body shape variation. Our observation that IHC, WC, and WHR polygenic scores follow a strong latitudinal cline in Western Eurasia support the role of natural selection in establishing Bergmann's Rule in humans, and are consistent with thermoregulatory adaptation in response to latitudinal temperature variation.
From the paper:
... To explore whether patterns observed in the polygenic scores were caused by natural selection, we tested whether the observed distribution of polygenic scores across populations could plausibly have been generated under a neutral model of genetic drift ...

The study of polygenic adaptation provides new avenues for the study of human evolution, and promises a synthesis of physical anthropology and human genetics. Here, we provide the first population genetic evidence for selected divergence in height polygenic scores among Asian populations. We also provide evidence of selected divergence in IHC and WHR polygenic scores within Europe and to a lesser extent Asia, and show that both hip and waist circumference have likely been influenced by correlated selection on height and waist-hip ratio. Finally, signals of divergence among Asian populations can be explained in terms of differential relatedness to Europeans, which suggests that much of the divergence we detect predates the major demographic events in the history of modern Eurasian populations, and represents differential inheritance from ancient populations which had already diverged at the time of admixture. ...

Sunday, July 23, 2017

Pleiotropy, balancing selection, and all that: heart disease

This paper suggests that some genetic variants which increase risk of coronary artery disease (CAD) have been maintained in the population because of their positive effects in other areas of fitness, such as reproduction.
Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy

Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the relationship between CAD and lifetime reproductive success is antagonistic. This supports the presence of antagonistic-pleiotropic tradeoffs on CAD loci and provides a novel explanation for the maintenance and high prevalence of CAD in modern humans. Lastly, we found that positive selection more often targeted CAD gene regulatory variants using HapMap3 lymphoblastoid cell lines, which further highlights the unique biological significance of candidate adaptive loci underlying CAD. Our study provides a novel approach for detecting selection on polygenic traits and evidence that modern human genomes have evolved in response to CAD-induced selection pressures and other early-life traits sharing pleiotropic links with CAD.

Author summary

How genetic variation contributes to disease is complex, especially for those such as coronary artery disease (CAD) that develop over the lifetime of individuals. One of the fundamental questions about CAD––whose progression begins in young adults with arterial plaque accumulation leading to life-threatening outcomes later in life––is why natural selection has not removed or reduced this costly disease. It is the leading cause of death worldwide and has been present in human populations for thousands of years, implying considerable pressures that natural selection should have operated on. Our study provides new evidence that genes underlying CAD have recently been modified by natural selection and that these same genes uniquely and extensively contribute to human reproduction, which suggests that natural selection may have maintained genetic variation contributing to CAD because of its beneficial effects on fitness. This study provides novel evidence that CAD has been maintained in modern humans as a by-product of the fitness advantages those genes provide early in human lifecycles.
From the paper:
... research in quantitative genetics has shown that rapid adaptation can often occur on complex traits that are highly polygenic [29, 30]. Under the ‘infinitesimal (polygenic) model’, such traits are likely to respond quickly to changing selective pressures through smaller allele frequency shifts in many polymorphisms already present in the population [13, 31].

To test for selection signals for variants directly linked with CAD, we utilized SNP summary statistics from 56 genome-wide significant CAD loci in Nikpay et al. [40], the most recent and largest CAD case-control GWAS meta-analysis to date, to identify 76 candidate genes for CAD (see Methods). Nikpay used 60,801 CAD cases and 123,504 controls ...

For a subset of CAD loci, we found significant quantitative associations between disease risk and selection signals and for each of these the direction of this association was often consistent between populations ...

In the comparison across populations, directionality of significant selection-risk associations tended to be most consistent for populations within the same ancestral group (Fig 1B). For example, in PHACTR1, negative associations were present within all European populations (CEU, TSI, FIN), and in NT5C2 strong positive associations were present in all East Asian populations (CHB, CHD, JPT). Other negative associations that were consistent across all populations within an ancestry group included five genes in Europeans (COG5, ABO, ANKS1A, KSR2, FLT1) and four genes (LDLR, PEMT, KIAA1462, PDGFD) in East Asians. ...

... By comparing positive selection variation with genetic risk variation at known loci underlying CAD, we were able to identify and prioritize genes that have been the most likely targets of selection related to this disease across diverse human populations. That selection signals and the direction of selection-risk relationships varied among some populations suggests that CAD-driven selection has operated differently in these populations and thus that these populations might respond differently to similar heart disease prevention strategies. The pleiotropic effects that genes associated with CAD have on traits associated with reproduction that are expressed early in life strongly suggests some of the evolutionary reasons for the existence of human vulnerability to CAD.
Bonus: ~300 variants control about 20% of total variance in genetic CAD risk. This means polygenic risk predictors will eventually have a strong correlation (e.g., at least ~0.4 or 0.5) with actual risk. Good enough for identification of outliers.
Nature Genetics (2017) doi:10.1038/ng.3913

Genome-wide association studies (GWAS) in coronary artery disease (CAD) had identified 66 loci at 'genome-wide significance' (P < 5 × 10−8) at the time of this analysis, but a much larger number of putative loci at a false discovery rate (FDR) of 5% (refs. 1,2,3,4). Here we leverage an interim release of UK Biobank (UKBB) data to evaluate the validity of the FDR approach. We tested a CAD phenotype inclusive of angina (SOFT; ncases = 10,801) as well as a stricter definition without angina (HARD; ncases = 6,482) and selected cases with the former phenotype to conduct a meta-analysis using the two most recent CAD GWAS2, 3. This approach identified 13 new loci at genome-wide significance, 12 of which were on our previous list of loci meeting the 5% FDR threshold2, thus providing strong support that the remaining loci identified by FDR represent genuine signals. The 304 independent variants associated at 5% FDR in this study explain 21.2% of CAD heritability and identify 243 loci that implicate pathways in blood vessel morphogenesis as well as lipid metabolism, nitric oxide signaling and inflammation.
This is a recent review article (2016):
Genetics of Coronary Artery Disease ...Overall, recent studies have led to a broader understanding of the genetic architecture of CAD and demonstrate that it largely derives from the cumulative effect of multiple common risk alleles individually of small effect size rather than rare variants with large effects on CAD risk. Despite this success, there has been limited progress in understanding the function of the novel loci; the majority of which are in noncoding regions of the genome.

Tuesday, July 18, 2017

Don't Touch the Computer

Under what circumstances should humans override algorithms?

From what I have read I doubt that a hybrid team of human + AlphGo would perform much better than AlphaGo itself. Perhaps worse, depending on the epistemic sophistication and self-awareness of the human. In hybrid chess it seems that the ELO score of the human partner is not the main factor, but rather an understanding of the chess program, its strengths, and limitations.

Unless I'm mistaken the author of the article below sometimes comments here.
Don’t Touch the Computer
By Jason Collins

... Some interpret this unique partnership to be a harbinger of human-machine interaction. The superior decision maker is neither man nor machine, but a team of both. As McAfee and Brynjolfsson put it, “people still have a great deal to offer the game of chess at its highest levels once they’re allowed to race with machines, instead of purely against them.”

However, this is not where we will leave this story. For one, the gap between the best freestyle teams and the best software is closing, if not closed. As Cowen notes, the natural evolution of the human-machine relationship is from a machine that doesn’t add much, to a machine that benefits from human help, to a machine that occasionally needs a tiny bit of guidance, to a machine that we should leave alone.

But more importantly, let me suppose we are going to hold a freestyle chess tournament involving the people reading this article. Do you believe you could improve your chance of winning by overruling your 3300-rated chess program? For nearly all of us, we are best off knowing our limits and leaving the chess pieces alone.

... We interfere too often, ... This has been documented across areas from incorrect psychiatric diagnoses to freestyle chess players messing up their previously strong position, against the advice of their supercomputer teammate.

For example, one study by Berkeley Dietvorst and friends asked experimental subjects to predict the success of MBA students based on data such as undergraduate scores, measures of interview quality, and work experience. They first had the opportunity to do some practice questions. They were also provided with an algorithm designed to predict MBA success and its practice answers—generally far superior to the human subjects’.

In their prediction task, the subjects had the option of using the algorithm, which they had already seen was better than them in predicting performance. But they generally didn’t use it, costing them the money they would have received for accuracy. The authors of the paper suggested that when experimental subjects saw the practice answers from the algorithm, they focussed on its apparently stupid mistakes—far more than they focussed on their own more regular mistakes.

Although somewhat under-explored, this study is typical of when people are given the results of an algorithm or statistical method (see here, here, here, and here). The algorithm tends to improve their performance, yet the algorithm by itself has greater accuracy. This suggests the most accurate method is often to fire the human and rely on the algorithm alone. ...

Saturday, July 15, 2017

Genetic variation in Han Chinese population

Largest component of genetic variation is a N-S cline (phenotypic N-S gradient discussed here). Variance accounted for by second (E-W) PC vector is much smaller and the Han population is fairly homogeneous in genetic terms: ...while we revealed East-to-West structure among the Han Chinese, the signal is relatively weak and very little structure is discernible beyond the second PC (p.24).

Neandertal ancestry does not vary significantly across provinces, consistent with admixture prior to the dispersal of modern Han Chinese.
A comprehensive map of genetic variation in the world's largest ethnic group - Han Chinese

As are most non-European populations around the globe, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our dataset. Individuals from our study come from 19 out of 22 provinces across China, allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identify previously unrecognized population structure along the East-West axis of China and report unique signals of admixture across geographical space, such as European influences among the Northwestern provinces of China. Finally, we identified a number of highly differentiated loci, indicative of local adaptation in the Han Chinese. In particular, we detected extreme differentiation among the Han Chinese at MTHFR, ADH7, and FADS loci, suggesting that these loci may not be specifically selected in Tibetan and Inuit populations as previously suggested. On the other hand, we find that Neandertal ancestry does not vary significantly across the provinces, consistent with admixture prior to the dispersal of modern Han Chinese. Furthermore, contrary to a previous report, Neandertal ancestry does not explain a significant amount of heritability in depression. Our findings provide the largest genetic data set so far made available for Han Chinese and provide insights into the history and population structure of the world's largest ethnic group.
See also Large-Scale Psychological Differences Within China.

The Loveless (1982) and Born to Run

The Loveless (free now on Amazon Prime) was the first film directed by Kathryn Bigelow (Point Break, Zero Dark Thirty) and also the first first film role for a young Willem Dafoe. Dafoe has more leading man star power in this role than in most of his subsequent work.

Loveless was shot in 22 days, when Bigelow was fresh out of Columbia film school. The movie could be characterized as a biker art film with some camp elements, but overall a fairly dark and nihilistic mood. The video above is a fan mash up of Loveless and Bruce Springsteen's Born to Run. It works well on its own terms, although Born to Run is more romantic than nihilistic, at least musically. The lyrics by themselves, however, fit the film rather well.
Born To Run

Bruce Springsteen

At night we ride through the mansions of glory in suicide machines
Sprung from cages out on highway nine,
H-Oh, Baby this town rips the bones from your back
It's a death trap, it's a suicide rap
We gotta get out while we're young
`Cause tramps like us, baby we were born to run

Yes, girl we were

Wendy let me in I wanna be your friend
I want to guard your dreams and visions
Just wrap your legs 'round these velvet rims
And strap your hands 'cross my engines
Together we could break this trap
We'll run till we drop, baby we'll never go back
H-Oh, Will you walk with me out on the wire
`Cause baby I'm just a scared and lonely rider
But I gotta know how it feels
I want to know if love is wild
Babe I want to know if love is real

Oh, can you show me

Beyond the Palace hemi-powered drones scream down the boulevard
Girls comb their hair in rearview mirrors
And the boys try to look so hard
The amusement park rises bold and stark
Kids are huddled on the beach in a mist
I wanna die with you Wendy on the street tonight
In an everlasting kiss

One, two, three, four

The highway's jammed with broken heroes on a last chance power drive
Everybody's out on the run tonight
But there's no place left to hide
Together Wendy we can live with the sadness
I'll love you with all the madness in my soul
H-Oh, Someday girl I don't know when
We're gonna get to that place
Where we really wanna go
And we'll walk in the sun
But till then tramps like us
Baby we were born to run
Oh honey, tramps like us
Baby we were born to run
Come on with me, tramps like us
Baby we were born to run

Thursday, July 13, 2017

Super-human Relational Reasoning (DeepMind)

These neural nets reached super-human (better than an average human) performance on tasks requiring relational reasoning. See the short video for examples.
A simple neural network module for relational reasoning

Adam Santoro, David Raposo, David G.T. Barrett, Mateusz Malinowski, Razvan Pascanu, Peter Battaglia, Timothy Lillicrap (Submitted on 5 Jun 2017)

Relational reasoning is a central component of generally intelligent behavior, but has proven difficult for neural networks to learn. In this paper we describe how to use Relation Networks (RNs) as a simple plug-and-play module to solve problems that fundamentally hinge on relational reasoning. We tested RN-augmented networks on three tasks: visual question answering using a challenging dataset called CLEVR, on which we achieve state-of-the-art, super-human performance; text-based question answering using the bAbI suite of tasks; and complex reasoning about dynamic physical systems. Then, using a curated dataset called Sort-of-CLEVR we show that powerful convolutional networks do not have a general capacity to solve relational questions, but can gain this capacity when augmented with RNs. Our work shows how a deep learning architecture equipped with an RN module can implicitly discover and learn to reason about entities and their relations.

Tuesday, July 11, 2017

Probing deep networks: inside the black box

See also AI knows best: AlphaGo "like a God":

Sunday, July 09, 2017

Yoel Romero, freak athlete

Romero is 40 years old! He is a former World Champion and Olympic silver medalist for Cuba in freestyle wrestling. Watch the video -- it's great! :-)

He lost a close championship fight yesterday in the UFC at 185lbs. The guy he lost to, Robert Whittaker, is a young talent and a class act. It's been said that Romero relies too much on athleticism and doesn't fight smart (this goes back to his wrestling days). He should have attacked Whittaker more ruthlessly after he hurt Whittaker's knee early in the fight with a kick.

Saturday, July 08, 2017

Politico: Trump could have won as a Democrat

I'm old enough to have been aware of Donald Trump since before the publication of Art of the Deal in 1987. In these decades, during which he was one of the best known celebrities in America, he was largely regarded as a progressive New Yorker, someone who could easily pass as a rich Democrat. Indeed, he was friendly with the Clintons -- Ivanka and Chelsea are good friends. There were no accusations of racism, and he enjoyed an 11 year run (2004-2015) on The Apprentice. No one would have doubted for a second that he was an American patriot, the least likely stooge for Russia or the USSR. I say all this to remind people that the image of Trump promulgated by the media and his other political enemies since he decided to run for President is entirely a creation of the last year or two.

If you consider yourself a smart person, a rational person, an evidence-driven person, you should reconsider whether 30+ years of reporting on Trump is more likely to be accurate (during this time he was a public figure, major celebrity, and tabloid fodder: subject to intense scrutiny), or 1-2 years of heavily motivated fake news.

In the article below, Politico considers the very real possibility that Trump could have run, and won, as a Democrat. If you're a HATE HATE HATE NEVER NEVER TRUMP person, think about that for a while.
Politico: ... Could Trump have done to the Democrats in 2016 what he did to the Republicans? Why not? There, too, he would have challenged an overconfident, message-challenged establishment candidate (Hillary Clinton instead of Jeb Bush) and with an even smaller number of other competitors to dispatch. One could easily see him doing as well or better than Bernie Sanders—surprising Clinton in the Iowa caucuses, winning the New Hampshire primaries, and on and on. More to the point, many of Trump’s views—skepticism on trade, sympathetic to Planned Parenthood, opposition to the Iraq war, a focus on blue-collar workers in Rust Belt America—seemed to gel as well, if not better, with blue-state America than red. Think the Democrats wouldn’t tolerate misogynist rhetoric and boorish behavior from their leaders? Well, then you’ve forgotten about Woodrow Wilson and John F. Kennedy and LBJ and the last President Clinton.

There are, as with every what-if scenario, some flaws. Democrats would have deeply resented Trump’s ‘birther’ questioning of Barack Obama’s origins, and would have been highly skeptical of the former reality TV star’s political bona fides even if he hadn’t made a sharp turn to the right as he explored a presidential bid in the run up to the 2012 election. His comments on women and minorities would have exposed him to withering scrutiny among the left’s army of advocacy groups. Liberal donors would likely have banded together to strangle his candidacy in its cradle—if they weren’t laughing him off. But Republican elites tried both of these strategies in 2015, as well, and it manifestly didn’t work. What’s more, Trump did once hold a passel of progressive stances—and he had friendships all over the political map. As Bloomberg’s Josh Green notes, in his Apprentice days, Trump was even wildly popular among minorities. It’s not entirely crazy to imagine him outflanking a coronation-minded Hillary Clinton on the left and blitzing a weak Democratic field like General Sherman marching through Georgia. ...
See also Trump on Trump.

I voted twice for Bill Clinton and twice for Obama. Listen carefully: their positions on immigration, as expressed below, do not differ much in substance from Trump's.

Thursday, July 06, 2017

10 Years of GWAS Discovery

See post from 2012: Five years of GWAS discovery to see how far the field of human genomics has advanced in just a short time.
10 Years of GWAS Discovery: Biology, Function, and Translation

The American Journal of Human Genetics 101, 5–22, July 6, 2017

Peter M. Visscher,1,2,* Naomi R. Wray,1,2 Qian Zhang,1 Pamela Sklar,3 Mark I. McCarthy,4,5,6 Matthew A. Brown,7 and Jian Yang1,2

Application of the experimental design of genome-wide association studies (GWASs) is now 10 years old (young), and here we review the remarkable range of discoveries it has facilitated in population and complex-trait genetics, the biology of diseases, and translation toward new therapeutics. We predict the likely discoveries in the next 10 years, when GWASs will be based on millions of samples with array data imputed to a large fully sequenced reference panel and on hundreds of thousands of samples with whole-genome sequencing data.

Five years ago, a number of us reviewed (and gave our opinion on) the first 5 years of discoveries that came from the experimental design of the GWAS.1 That review sought to set the record straight on the discoveries made by GWASs because at that time, there was still a level of misunderstanding and distrust about the purpose of and discoveries made by GWASs. There is now much more acceptance of the experimental design because the empirical results have been robust and overwhelming, as reviewed here.

... GWAS results have now been reported for hundreds of complex traits across a wide range of domains, including common diseases, quantitative traits that are risk factors for disease, brain imaging phenotypes, genomic measures such as gene expression and DNA methylation, and social and behavioral traits such as subjective well-being and educational attainment. About 10,000 strong associations have been reported between genetic variants and one or more complex traits,10 where “strong” is defined as statistically significant at the genome-wide p value threshold of 5 × 10−8, excluding other genome-wide-significant SNPs in LD (r2 > 0.5) with the strongest association (Figure 2). GWAS associations have proven highly replicable, both within and between populations,11, 12 under the assumption of adequate sample sizes.

One unambiguous conclusion from GWASs is that for almost any complex trait that has been studied, many loci contribute to standing genetic variation. In other words, for most traits and diseases studied, the mutational target in the genome appears large so that polymorphisms in many genes contribute to genetic variation in the population. This means that, on average, the proportion of variance explained at the individual variants is small. Conversely, as predicted previously,1, 13 this observation implies that larger experimental sample sizes will lead to new discoveries, and that is exactly what has occurred over the last decade. ...

Tuesday, July 04, 2017

Building the Gadget: A Technical History of the Atomic Bomb

This is the best technical summary of the Los Alamos component of the Manhattan Project that I know of. It includes, for example, detail about the hydrodynamical issues that had to be overcome for successful implosion. That work drew heavily on von Neumann's expertise in shock waves, explosives, numerical solution of hydrodynamic partial differential equations, etc. A visit by G.I. Taylor alerted the designers to the possibility of instabilities in the shock front (Rayleigh–Taylor instability). Concern over these instabilities led to the solid-core design known as the Christy Gadget.

... Unlike earlier histories of Los Alamos, this book treats in detail the research and development that led to the implosion and gun weapons; the research in nuclear physics, chemistry, and metallurgy that enabled scientists to design these weapons; and the conception of the thermonuclear bomb, the "Super." Although fascinating in its own right, this story has particular interest because of its impact on subsequent devel- opments. Although many books examine the implications of Los Alamos for the development of a nuclear weapons culture, this is the first to study its role in the rise of the methodology of "big science" as carried out in large national laboratories.

... The principal reason that the technical history of Los Alamos has not yet been written is that even today, after half a century, much of the original documentation remains classified. With cooperation from the Los Alamos Laboratory, we received authorization to examine all the relevant documentation. The book then underwent a classification review that resulted in the removal from this edition of all textual material judged sensitive by the Department of Energy and all references to classified documents. (For this reason, a number of quotations appear without attribution.) However, the authorities removed little information. Thus, except for a small number of technical facts, this account represents the complete story. In every instance the deleted information was strictly technical; in no way has the Los Alamos Laboratory or the Department of Energy attempted to shape our interpretations. This is not, therefore, a "company history"; throughout the research and writing, we enjoyed intellectual freedom.

... Scientific research was an essential component of the new approach: the first atomic bombs could not have been built by engineers alone, for in no sense was developing these bombs an ordinary engineering task. Many gaps existed in the scientific knowledge needed to complete the bombs. Initially, no one knew whether an atomic weapon could be made. Furthermore, the necessary technology extended well beyond the "state of the art." Solving the technical problems required a heavy investment in basic research by top-level scientists trained to explore the unknown - scientists like Hans Bethe, Richard Feynman, Rudolf Peierls, Edward Teller, John von Neumann, Luis Alvarez, and George Kistiakowsky. To penetrate the scientific phenomena required a deep understanding of nuclear physics, chemistry, explosives, and hydrodynamics. Both theoreticians and experimentalists had to push their scientific tools far beyond their usual capabilities. For example, methods had to be developed to carry out numerical hydrodynamics calculations on a scale never before attempted, and experimentalists had to expand the sensitivity of their detectors into qualitatively new regimes.

... American physics continued to prosper throughout the 1920s and1930s, despite the Depression. Advances in quantum theory stimulated interest in the microscopic structure of matter, and in 1923 Robert Millikan of Caltech was awarded the Nobel Prize for his work on electrons. In the 1930s and 1940s, Oppenheimer taught quantum theory to large numbers of students at the Berkeley campus of the University of California as well as at Caltech. Also at Berkeley in the 1930s and 1940s, the entrepreneurial Lawrence gathered chemists, engineers, and physicists together in a laboratory where he built a series of ever-larger cyclotrons and led numerous projects in nuclear chemistry, nuclear physics, and medicine. By bringing together specialists from different fields to work cooperatively on large common projects, Lawrence helped to create a distinctly American collaborative research endeavor - centered on teams, as in the industrial research laboratories, but oriented toward basic studies without immediate application. This approach flourished during World War II.

Sunday, July 02, 2017

Machine intelligence threatens overpriced aircraft carriers

The excerpt below is from a recent comment thread, arguing that the US Navy should de-emphasize carrier groups in favor of subs and smaller surface ships. Technological trends such as rapid advancement in machine learning (ML) and sensors will render carriers increasingly vulnerable to missile attack in the coming decades.
1. US carriers are very vulnerable to *conventional* Russian and PRC missile (cruise, ASBM) weapons.

2. Within ~10y (i.e., well within projected service life of US carriers) I expect missile systems of the type currently only possessed by Russia and PRC to be available to lesser powers. I expect that a road-mobile ASBM weapon with good sensor/ML capability, range ~1500km, will be available for ~$10M. Given a rough (~10km accuracy) fix on a carrier, this missile will be able to arrive in that area and then use ML/sensors for final targeting. There is no easy defense against such weapons. Cruise missiles which pose a similar threat will also be exported. This will force the US to be much more conservative in the use of its carriers, not just against Russia and PRC, but against smaller countries as well.

Given 1. and 2. my recommendation is to decrease the number of US carriers and divert the funds into smaller missile ships, subs, drones, etc. Technological trends simply do not favor carriers as a weapon platform.

Basic missile technology is old, well-understood, and already inexpensive (compared, e.g., to the cost of fighter jets). ML/sensor capability is evolving rapidly and will be enormously better in 10y. Imagine a Mach 10 robot kamikaze with no problem locating a carrier from 10km distance (on a clear day there are no countermeasures against visual targeting using the equivalent of a cheap iPhone camera -- i.e., robot pilot looks down at the ocean to find carrier), and capable of maneuver. Despite BS claims over the years (and over $100B spent by the US), anti-missile technology is not effective, particularly against fast-moving ballistic missiles.

One only has to localize the carrier to within few x 10km for initial launch, letting the smart final targeting do the rest. The initial targeting location can be obtained through many methods, including aircraft/drone probes, targeting overflight by another kind of missile, LEO micro-satellites, or even (surreptitious) cooperation from Russia/PRC (or a commercial vendor!) via their satellite network.
Some relevant links, supplied by a reader. 1. National Air and Space Intelligence Center report on ballistic and cruise missile threats (note the large number of countries that can utilize basic missile technology; all they need is an ML/sensor upgrade...), and 2. Stop the Navy's carrier plan by Capt. Jerry Hendrix (ret.), director of the Defense Strategies and Assessments Program at the Center for a New American Security:
... the Navy plans to modernize its carrier program by launching a new wave of even larger and more expensive ships, starting with the USS Gerald Ford, which cost $15 billion to build — by far the most expensive vessel in naval history. This is a mistake: Because of changes in warfare and technology, in any future military entanglement with a foe like China, current carriers and their air wings will be almost useless and the next generation may fare even worse.

... The average cost of each of the 10 Nimitz class carriers was around $5 billion. When the cost of new electrical systems is factored in, the USS Ford cost three times as much and took five years to build. With the deficit projected to rise considerably over the next decade, defense spending is unlikely to receive a significant bump. Funding these carriers will crowd out spending on other military priorities, like the replacement of the Ohio class ballistic missile submarine, perhaps the most survivable and important leg of our strategic deterrent triad. There simply isn’t room to fund an aircraft carrier that costs the equivalent of the entire Navy shipbuilding budget.

... The Navy’s decision on the carriers today will affect U.S. naval power for decades. These carriers are expected to be combat effective in 2065 — over 150 years since the idea of an aircraft carrier was first conceived. ...
See also Defense Science Board report on Autonomous Systems.

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