Bonobo toolmaking hints glimpses of “cutting edge” stone age technology

This is really cool as human ancestors, many millions of years ago, my have started making tools in very similar fashion. Here is the Roffman et al. PNAS paper that describes the findings in detail.

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Genomics for future anthropologists & archeologists

An awesome use of genomics and proteomics in archeology and paleopathogenomics (yes I just invented the word!)

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Origin of species: through gene regulation?

“How does evolution occur?” This has been a central question in biology. Does evolution occur because a new mutation results in a new protein or because the same gene is regulated differently? How do new morphological structures evolve? How does speciation occur? A recent paper in Science ties principles in evolutionary biology, development biology, and molecular biology to answer these exact questions.

Distalless protein (dll), which is highly conserved across many genera, seems to have EVOLVED A NOVEL FUNCTION in a particular species of insect (Rheumatobates rileyi) to generate male specific antennal appendages. Males possessing these appendages have increased chances of reproducing therefore, have higher fitness (see video below). There could be two reasons for the development of these antennal appendages: first, dll in this particular species is shorter than all other species and second, dll is differentially regulated in this species. Although dll in R. rileyi appears to be shortened,  I feel that its differential expression may be more important in creating this morphology. dll is an important protein in development and therefore, it is pleiotrophic (see figure on the right below). Thus, it is likely that any alteration of the original function by the shortened protein would result in death. One scenario could be that a cis-mediated regulatory change in dll expression causes it to be expressed at a novel developmental stage in a novel tissue where some other male-specific proteins are also expressed. Interactions between dll and such male-specific protein(s) results in the formation of antennal appandages.

So, what does this study tell us about how evolution occurs? Well, one way evolution by natural selection occurs is not through new mutations that alters the function of existing proteins but through mutations that result in modifications in regulation of existing proteins to acquire novel function. Existing proteins may acquire novel functions if they are ectopically expressed, i.e, in developmental stages or tissues where they are normally not expressed. Most of the times ectopic expression may either provide no benefit to the individuals or even be detrimental but sometimes, ectopic expression may allow these proteins to interact with other proteins expressed in that tissue at that developmental stage to perform new functions. This new function may confer some reproductive advantage to that individual, therefore enhancing what population geneticists/evolutionary biologists call ‘fitness’. Over time, these individuals will take over in the population. If this population remains isolated from the ancestral population for a long period of time, it may give rise to a novel species (not this study but can be imagined).

This is a cool example of how integrating many areas of biology (evolutionary, developmental, molecular, and entomology) can elucidate novel genetic mechanisms underlying phenotypic diversity.

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Modern human diseases and demographics

Tumultuous effects resulted and continue to result from the massive mixing of the world’s biota when European ships reconnected the American continent to the rest of the world.  Mann traced several of the cascading consequences of “the biggest ecological convulsion since the death of the dinosaurs.”
The first momentous change came from microbial exchange—20 lethal diseases came from Europe to the Americas while only one (syphilis) went the other way.  North America, which had been largely cleared by natives with fire and agriculture, reforested when two-thirds to 95% of the native inhabitants died from European diseases—”the greatest demographic catastrophe in human history.”  That huge reforesting drew down atmospheric carbon dioxide and Europe’s “Little Ice Age” (1550-1800) apparently resulted.
Meanwhile the mountain of silver at Potosí, Bolivia, vastly enriched Europe, which “went shopping” worldwide.  Trading ships coursed the world’s oceans.  One artifact picked up from Peru was the potato—a single variety of the  6,000 available.  When potatoes in Europe turned out to provide four times the amount of food per acre as wheat, the previously routine famines came to an end, population soared, governments became more stable, and they began building global empires.  After 1843 guano shipped by the ton from coastal Peru for fertilizer introduced high-input agriculture.  In Ireland 40% of the exploding population ate only potatoes.  Around 1844 a potato blight arrived from Mexico, and a million Irish died in the Great Famine and a million more emigrated.
In China, which has no large lakes and only two major rivers, agriculture had been limited to two wet regions where rice could be grown.  Two imports from America—maize and sweet potato—could be farmed in dry lands.  As in Europe, population went up.  Vast areas were terraced as Han farmers pushed westward as far as the Mongolian desert.  In heavy rains the terraces melted into the streams, and silt built up in the lowlands, elevating the rivers as much as 40 feet above the surrounding terrain, so when they flooded, millions died.  “A Katrina per month for 100 years,” as one Chinese meteorologist described it.  The constant calamities weakened the government, and China became ripe for foreign colonial takeover.
In America two imported diseases—malaria and yellow fever—were selective in who they killed.  Europeans died in huge numbers, but Africans were one-tenth as susceptible, and so slavery replaced traditional indentured servitude in all the warm regions that favored mosquito-borne diseases.  As one result, four times as many Africans as Europeans crossed the Atlantic and began mixing with the remaining native Americans, giving rise to an endless variety of racial blends and accompanying vitality throughout the Americas.
During the Q & A, Mann described a potential fresh eco-convulsion-in-waiting.  “There is an area in southeast Asia roughly the size of Great Britain that is a single giant rubber plantation.”  Where rubber trees originally came from in the Amazon there is now a rubber tree leaf-blight that is starting to spread in Asia.  “You could lose all the rubber trees in three to six months.  It would be the biggest deforestation in a long time.”  The entire auto industry, he added, depends on just-in-time delivery of rubber.
Stuart Brand’s summary of Charles C. Mann’s talk at The Longnow Foundation in April 2012. I decided to post it because it is one of the most eloquently articulated account of the modern history of Homo sapiens.

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Phylo: Crowdsourcing BIOINFORMATICS and GENOMICS

For many reasons multiple species DNA alignment is a hard problem. One reason it is hard is because as evolutionary relationship between organisms increase, the similarities in their DNA sequence decrease. Many times we encounter gaps and duplications that make accurate alignment very difficult.

Computer algorithms are getting better (compare CLUSTAL-W to  Clustal Omega), it is still pretty darn difficult to accurately align multiple species. A lot of time and effort is needed to manually inspect alignments performed even by the best multiple species aligner. A handful of scientists can only take it so far…so, crowdsourcing helps here.

One can use an algorithm to perform multiple species alignments of multiple genomes. These alignments can then be made publicly available to public such that they can, in their leisure, improve them by manually intervention. Recently, I came across PHYLO which is a GAME, yes a  GAME!!!! in which multiple species alignments of human genome that are potentially linked to various genetic disorders, such as breast cancer can be manually curated by the public. “Every alignment is received, analyzed, and stored in a database, where it will eventually be re-introduced back into the global alignment as an optimization.”

This is a wonderful opportunity for the public to learn a little about bioinformatics and to understand about evolution. So folks, substitute your AngryBirds with Phylo and help yourself increase your chances of living longer by helping the scientific community move closer towards finding ‘cures’ for these diseases.

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Visualizing biology: from conception to birth, cell division, and more

Visualization helps in learning anything. In biology visualization has traditionally been done using pictures or posters (right).
From conception to birth. But that is so 1970s. In the technocratic future, where lullabies are delivered via iPod and iPads are norm in kindergarten, figures or posters wond do any good. Kids would hate to learn from static images….they need videos! And if you are making videos, you might as well use real data…and Alexander Tsiaras does exactly that. Using advanced technology on real pregnant women he captures images of life from conception to birth. Mes merizing!

Okay, let’s take it to a molecular level now. Let us look at structure of DNA, cell division, and molecular machinery of cell division:

Cant have enough? Visit Drew Berry’s page.

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Many years ago (2003), Steve Robison, then co-ordinator of the Associated Students of College of San Mateo (ASCSM) told me about his dream of establishing a free and self-sustaining university. His envisioned students practicing what they learn in classes to support the campus community thus making it sustainable. For example, culinary students will prepare meals, horticulturalists/botanists will maintain the gardens, architects will design new buildings and so on. At that time this idea of free education seemed a distant possibility.

But now, free education is the new trend. Unlike Steve’s model of a physically existing self-sustaining university, a few successful free ‘universities’ have emerged over the internet. Salman Khan’s Khan Academy definitely led the way by providing free and easy to understand tutorials over the internet. His materials were so awesome that Bill Gates announced he was a huge fan on national TV. MIT has been offering free online classes over the internet for a number of years and recently MIT has launched MITx, a program that provides students with “the opportunity to demonstrate their mastery of the material and earn a certificate from MITx” for a class titled Circuits and Electronics.

Being originally from Nepal, a country that suffers severe higher secondary education bottleneck, I became very excited when I first heard of MITx. So I tweeted it and put it as my facebook status. But I was thrilled to hear that MITx was not the first online university and two artificial intelligence professors at Standford are doing something even better!

Sebastian Thrun and Peter Norvig heard Salman Khan give a talk at TED and launched their own academy at Stanford which is now becoming Udacity, a free university to learn computer programming language and artificial intelligence. The best thing about Udacity is that if you are the top student in their classes you may have a job waiting for you in the leading industries in the world.

Salman Khan: Let's use video to reinvent education (TED talks)

What does Udacity mean to students in the US?
I think this is a revolution in education. For hundreds of years many students have tried to buy university brand names by paying thousands of dollars in tuition. The higher the brand name of an University, higher the tuition fees. Two incentives to pay such outrageous fees are: the university name and networking with the alumni. Third minor incentive is the quality of education. Ultimately, the hopes of new graduates is to land a good job in a leading company. Unfortunately, none of the Universities care if you do not get a job. Once you graduate (and pay all the fees without which you dont graduate), the only correspondence you get is from alumni association asking for donation.

The cool thing about Udacity is that instead of earning money from student tuition, they make their money by helping students get a job. According to Wired, this is how it works: large companies pay 10-30% of an engineers’ first year salary to employment agencies. Udacity may generate most of their income from such companies by helping their top student obtain jobs. So, the education is free but money to run the university comes from top multibillion dollar companies. This cannot get more sweeter.

What does Udacity mean to the world?
If the world’s smartest person was born in a remote village in the middle of a mountain, (s)he may never realize her/his potential because the opportunity to learn is so little. Even if we imagine a 100% literate world, lack of high schools and universities forces many intelligent students worldwide to choose jobs that is far below their potential. Only a few lucky ones with enough collateral get visas to come to a developed country for higher education. Thus we are wasting talent with current educational model.

In theory, universities such as Udacity revolutionize education for the brilliant students in every corner of the world. Even if you were born in Mustang, a remotest state in the Himalayas, you can be taking a class in artificial intelligence and be admired by two best AI experts in the world. If you excel companies such as Google may be vying to hire you to design a driverless car. This is not a distant possibility; this is a commonplace at Udacity. Hence, it is an educational revolution.

On the incongruence between theory and practice
Free internet education has tremendous discrepancies between its hypothesized potential and realized potential in the global sense. Yes, we in theory it has tremendous potential but in practice, very few countries in the developing world are using it. According to World Internet Stats, the use of internet is the lowest in Africa followed by Asia with only 14% and 26% of the population using internet (average world-wide internet use 33%). Furthermore, this statistic is further inflated by developed nations both Asia (China, India, Japan) and Africa (South Africa). On a country level, of the 58 African countries, only 5 countries in Africa (9% African countries) have more than 5% internet users whereas 46 countries (81% African countries) have less than 1% internet users. Similarly, of the 35 Asian countries, only 4 (11.4% Asian countries) have over 5% and 23 (66% Asian countries) have less than 1% internet users. These statistics are corroborated by statistics from Khan Academy: virtually all of Khan Academy users are in developed countries.

The lack of internet use in developing countries is because of lack of infrastructure. Most countries in Asia and Africa are devoid of DSL. Because of geography, it is difficult and expensive to build infrastructure in most developing countries; hence telephone lines are nonexistent. Without telephone and DSL, most people in developing nations are without internet.

A simple to do list
Industrial revolution wedged a huge gap between the developed and developing nations. Internet revolution will forge a bigger gap if developing nations do not act now. Those nations that have nationwide internet service will benefit by incorporating internet in economics, communication, media, and education. Merchants in the developing countries with internet will be communicating globally and trading in dollars, whereas those in countries will be wasting their goods because they cannot sell all of it locally. More importantly, students in the countries will be using internet to learn about Salman Khans and Bill Gateses and interacting with Sebastian Thruns and Peter Norvigs and aspiring to land jobs in Googles and Bidus. Those in countries without internet will be struggling to find inspirations from their corrupt local leaders. Yes building internet infrastructure is expensive but since mobile phones are becoming increasing popular, investing in broadband services to increase internet users is a must for developing nations.

I have no faith in the corrupt politicians of developing countries; hence I do not expect the narrow-minded government depleted of visionary leaders to bring any positive changes in near future. Also, most NGOs are top heavy (spending 70% of their budget paying their executive staff) and can do little. The most important constituents to bring any change will be local entrepreneurs. Providing grants or microloans to encourage educators and businessmen to incorporate internet in their daily lives may bring innovative methods of increasing internet use in developing countries. For example, Mahabir Pun, a Raymond Magsaysay awardee has incorporated internet in education, animal breeding, monitoring global warming, and tele-medecine (more on Pun’s work).

Khan Academy and Udacity are not only great resources for youth and students worldwide but Udacity’s model of harvesting talent from all corners of the world can also be beneficial for companies. Hence, large companies should explore the opportunities of investing in internet infrastructure in developing nations because it is in their interest to find hidden talents and hire them. May be there are Marc Zuckerbergs and Sergey Brins somewhere in the Sahara desert in Chad and the mountains of Nepal, with 1.8% and 7% internet users respectively.

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