Is Artificial Intelligence a Threat to Mankind?

Artificial intelligenceTechnology: We all use it, and some of us couldn’t go an entire day without it. In many ways, digital technology has improved our lives by increasing productivity and communication. Computer technology is everywhere: our homes, offices, phones and even cars. Technology has integrating into our lives so completely that most of us no longer stop to marvel at even the [seemingly] simplest capabilities such as the predictive software that our smart phones use to predict which word we are typing after we type in only the first few letters, especially if the software gets it wrong much of the time. However, digital technology has its dangers and inconveniences: cybercrime, hackers, stolen data, and computer crashes and failed Wi-Fi connections at the most inopportune times. In a recent BBC interview, one of modern science’s most brilliant minds highlighted another potential danger: artificial intelligence. Does artificial intelligence pose a threat to mankind?

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Welcome to the Anthropocene? Only a Retrospective Analysis Will Tell

512px-Geologic_Clock_with_events_and_periods.svg

The 4.54 billion-year history of the earth is divided into many subdivisions: eons, eras, periods, epochs, and ages with each division representing a smaller chunk of geologic time. If you are a parent of a young child and you happen to have viewed several episodes of the children’s educational program Dinosaur Train, you are probably familiar with the Mesozoic Era and the Triassic, Jurassic and Cretaceous periods.

Geologic history is recorded in rocks—layer upon layer accumulates, each layer revealing the geological, ecological and biological events that occurred over the time period that it was deposited. These geologic records tell us about the plants and animal life that could be found hundreds, thousands or millions of years ago. The minerals and chemicals of the rocks can tell us about climate, and sudden changes in the rock layers can tell us about sudden changes on earth.

Many natural forces have shaped the Earth that we know today. Bombardment from extra-planetary objects has left craters and correlate mass extinction events in the geologic record (1). Oceans once covered areas that are now prairies, where if you look long enough or deep enough you might just find a fossil of a previously unknown fish (2). Wind has shaped the earth by eroding and depositing soil. The Loess Hills of western Iowa, USA, (3) and the Loess Plateau of China (4) are two examples of wind-created land forms each created by the slow, wind-driven deposition of soil particles. Of course, water too, is a major force for creating canyons and gorges. The Indus River in Asia, for instance, has been estimated to deepen its course between 2 and 12mm/year in the gorge areas and is capable of removing blocks of rocks measuring up to 70cm (5), and the Grand Canyon in the United States was formed by the erosive power of the Colorado River (6).

So clearly, the forces of Nature on Earth and the occasional meteor from space have played major roles in shaping the Earth that we climb, dive, hike, bike and stroll on today. However, is Nature still the major force at working shaping the Earth? Or is the human species assuming that role?

Continue reading “Welcome to the Anthropocene? Only a Retrospective Analysis Will Tell”

Dark Chocolate Benefits Improved by Fiber

Add pomegranate to your chocolate, says researcher Finley, to aid it's digestion, health benefits.
Add pomegranate to your chocolate, says researcher Finley, to aid it’s digestion and health benefits.

For chocolate lovers (and chocolate makers) it has been a great decade or so. Scientific research continues to prove what our brains have been saying for years; chocolate really IS good for us.

Research over the past decade or so has studied dark chocolate and its polyphenolic compounds, such as catechin and epicatechin, for their effects on inflammation, and cardiac and endothelial cell function. Today, from the American Chemical Society meeting in Dallas, TX, we learn new details about how dark chocolate brings its health benefits.

Before beneficial compounds in dark chocolate can reach the heart and other tissues in the body, digestive processes must occur to release the beneficial compounds from the chocolate.

Researcher John Finley and cohorts from Louisiana State University created a model digestive system by which to study what happens when cocoa combines with typical gut bacteria.

Their research showed that bacterial species in the colon ferment the fiber found in cocoa, which in turn aids in digestion of the larger polyphenols in cocoa, into smaller, more easily absorbed molecules. These smaller molecules, the catechins and epicatechins then enter the bloodstream and exert their anti-inflammatory effects.

Finley emphasized the role of dietary fiber, such as the fiber in the cocoa powders tested in this research, in the digestion process. He noted that prebiotics, carbohydrates in foods like raw garlic or cooked whole wheat flour, while not digested by humans, aid digestion and absorption of healthful food components, in this case polyphenols in dark chocolate.  Continue reading “Dark Chocolate Benefits Improved by Fiber”

Cell-free expression application: Screening for successful oligo-mediated knockdown design

800px-ZebrafischAlthough previous references have provided data regarding the potential oncogenic role of the gene ETV7, there has been minimal investigation as to its physiological role.
In the following reference, Quintana, A. et al. (2014) Disease Models & Mechanisms 7, 265–70, zebrafish were used as in vivo model system to characterize ETV7.

One key experiment required the morpholino-oligonucleotide -mediated knockdown of in vivo ETV7. Two independent morpholinos were designed: one that inhibited translation and the other that inhibited proper splicing of exon 3. The efficacy of the translation –blocking morpholino was assessed with cell free expression of ETV7-tagged with hemagglutinin (HA).

Western blot performed with anti-HA antibodies determined the extent of the knockdown compared to a control containing no morpholino added. Once an efficient design was determined via cell-free expression screening, it was used for in vivo experiments. In conjunction additional other techniques, concluded that ETV7 is essential for normal red blood cell development.

Cell-free Expression: A System for Every Need

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Cell-free protein expression is a simplified and accelerated avenue for the transcription and/or translation of a specific protein in a quasi cell environment. An alternative to slower, more cumbersome cell-based methods, cell-free protein expression methods are simple and fast and can overcome toxicity and solubility issues sometimes experienced in traditional E. coli expression systems. Continue reading “Cell-free Expression: A System for Every Need”

From Where, the Dog’s Ancient Ancestor

We’ve learned this year, 2013, that Europe may be the original home to domestic dogs, a title previously claimed by East Asia and the Middle East. A recent study published in Science magazine may put to rest the debate.

In their report, Thalmann and Wayne (1) used an evidential gold standard, DNA from mitochondria of fossilized ancient dog and wolf remains, to reach the conclusion that dogs originated from a now extinct line of European gray wolves.

In 2002, researchers from Sweden and China collaborated to compared first the mitochondrial DNA and later the complete mitochondrial genomes and Y chromosomes from a hundreds of wolves, coyotes and modern dogs from around the world (2). Their results showed the greatest genetic diversity from canids from East Asia. Such genetic diversity can be a marker of a species’ origin.

In 2010 Wayne, et al. (3) analyzed 48,000 markers from across the genome of gray wolves and dogs, again from around the world. The dogs were found to have more genetic material in common with Middle Eastern wolves than with those from East Asia. Wayne and colleagues found this a yes to dogs’ origins lying in the Middle East.

A criticism of the analysis done with modern dog DNA is that this DNA has been mixed with that from wolves. In addition, dog-dog breeding over the 15,000 to 30,000 years since this domestication, could confound results. Prior to the current study, critics called for analysis of ancient DNA remains only.

Wayne had collected DNA from ancient remains and due to recent collaboration with geneticist Thalmann, now had the lab-power to analyze those remains.

In this work, Wayne and Thalmann looked at mitochondrial DNA from ancient remains, those of 18 wolves and dogs. The fossils  ranging in age from 1,000 to 36,000 years. Eight of the samples were classified as dog-like and 10 samples were wolf-like in nature. They compared the ancient mitochondrial DNA samples to those of modern animals, including 77 dogs from an assortment of breeds, as well as 49 wolves and 4 coyotes. They then built a sort of a canid family tree, demonstrating relatedness in the animals whose DNA was analyzed.

Thalmann and Wayne’s finding showed that 1) the DNA of modern dogs more closely resembled that of ancient gray wolves than modern wolves, and 2) the geographic location of the wolves who’s DNA was most closely resembled, was Europe.

It is important to note that Thalmann and Wayne did not compare ancient remains from animals from the Middle East, nor did they have access to ancient remains from East Asia. In addition, there is criticism of the use of mitochondrial DNA, which represents only the maternal dog lineage. Thus there is more work to be done to finalize the ancestral home of the modern dog.

This work does, however, push back the origins of domesticated dogs to between 18,000 and 32,000 years ago, significant because the domestication timeline was previously believed to coincide with the rise of farming by our human ancestors. Domestic canines are now believed to have been part of humans lives far before farming was a way of life, back in the hunter-gatherer days.

There are those who believe that domestication of wolves, selectively bred to become modern dogs occurred simultaneously at more than one geographic region. Wolves were once found in many locations around the world and their usefulness to and domestication by humans would seem odd if only embraced by people from a single part of the world.

    References

  1. Thalmann, O. et al. Science (2013) 342, 871–874
  2. Savolainen P, Zhang YP, et al. (2002)
  3. Wayne, R.K. et al. (2010) Nature 464(7290), 898-902. 

Inheriting Fear: Mice Haunted by Parent’s Fears

baby miceImagine that you are sitting in your room when you smell cherries and you are suddenly, inexplicably afraid. Although odors can elicit strong emotional responses, you have no bad memories of cherries. What you don’t know is that your father did, and you have inherited his fear. Sound far fetched? Maybe not. A paper published in Nature Neuroscience found just such an inherited association in mice (1). Continue reading “Inheriting Fear: Mice Haunted by Parent’s Fears”

NanoLuc® Luciferase: A Good Thing for Small Packages

influenza viruses

A paper published on October 2 in the Journal of Virology describes an exciting development in the world of influenza research—the construction of a luciferase reporter virus that does not affect virulence and can be used to track development and spread of infection in mice.

Insertion of luciferase reporter genes into viruses has been accomplished before for several viruses, but has not been successful for influenza. Construction of influenza reporter viruses is complicated because the viral genome is small and all the viral genes are critical for infection. Therefore, replacement of an existing gene with a reporter gene or insertion of additional reporter sequences without affecting the virus’s ability to replicate and cause infection has proven difficult. To be successful, a reporter gene needs to be small enough to insert into the viral genome without eliminating any other vital functionality.

Continue reading “NanoLuc® Luciferase: A Good Thing for Small Packages”

Remembering Frederick Sanger and Sanger Sequencing

It is with sadness that we recognize the passing of Dr. Frederick Sanger. Sanger is known to molecular biologists and biochemists worldwide for his DNA sequencing technique, which won for him the 1980 Nobel prize in Chemistry.

Also noteworthy, Sanger’s laboratory accomplished the first complete genome sequence, that of a viral DNA genome more than 5,000 base pairs in length.

The 1980 prize was Sanger’s second Nobel award, his first awarded in 1958 for determining the chemical structure of proteins. In this work, Sanger elucidated not only the amino acids that comprised insulin but also the order in which the amino acids occurred.

About Sanger Sequencing
Sanger DNA sequencing is also known as the chain-termination method of sequencing. The Sanger technique uses dideoxynucleotides or ddNTPs in addition to typical deoxynucleotides (dNTPs) in the reaction. ddNTPs result in termination of the DNA strand because ddNTPs lack the 3’-OH group required for phosphodiester bond formation between nucleotides. Without this bond, the chain of nucleotides being formed is terminated.

Sanger sequencing requires a single-stranded DNA, a DNA primer (either radiolabeled or with a fluorescent tag), DNA polymerase, dNTPs and ddNTPs. Four reactions are set up, one for each nucleotide, G, A, T and C. In each reaction all four dNTPs are included, but only one ddNTP (ddATP, ddCTP, ddGTP or ddTTP) is added. The sequencing reactions are performed and the products denatured and separated by size using polyacrylamide gel electrophoresis.

Diagram of Sanger dideoxy sequencing. (Courtesy  of Wikipedia and Estevez, J.)
Diagram of Sanger dideoxy sequencing. (Courtesy of Wikipedia and Estevez, J.)

This reaction mix results in various lengths of fragments representing, for instance, the location of each A nucleotide in the sequence, because while there is more dATP than ddATP in the reaction, there is enough ddATP that each ATP ultimately instead is replaced with a ddATP, resulting in chain termination. Separation by gel electrophoresis reveals the size of these ddATP-containing fragments, and thus the locations of all A nucleotide in the sequence. Similar information is provided for GTP, CTP and TTP.

The Maxam and Gilbert DNA sequencing method had the advantage at the time of being used with double-stranded DNA. However, this method required DNA strand separation or fractionation of the restriction enzyme fragments, resulting in a somewhat more time-consuming technique, compared to the 1977 method published by Sanger et al.

Dr. Sanger was born in Gloucestershire, U.K. in 1918, the son of a physician. Though he initially planned to follow his father into medicine, biochemistry became his life-long passion and area of research endeavor. Sanger retired at age 65, to spend more time at hobbies of gardening and boating.

References

Sanger, F. , Nicklen, S. and Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74, 5463-7.

Maxam, A.M. and Gilbert, W. (1977) A New Method for Sequencing DNA. Proc. Natl. Acad. Sci. USA

There is something special about seeing the original Sanger publication from 1977, available here as a scan.

Articles, Blog Posts, Tweets, New Products and One Page to See Them All

If you are like me, there are just not enough hours in the day. The list of things that I need to get done regularly out distances the time I have to do them in. Keeping up with my favorite blogs, staying in tune with things on twitter and staying on top of new product and features often fall by the wayside because it takes so much time to go to all those pages and find the content I want.

Recently we updated the Promega PubHub page on our website with the hopes that it will help you use the time you spend visiting the PubHub page more efficiently. In addition to latest technical articles from Promega, useful lab facts and the ever-popular cartoons, we now offer a live feed of our Promega Connections Blog posts, tweets from @Promega and a list of new products.

PubHub2

We know that your time is valuable, and if you are interested in the articles and more from Promega, there is now one page to see it all.