Posts about science explained

How Lysozyme Protein in Our Tear-Drops Kill Bacteria

A disease-fighting protein in our teardrops has been tethered to a tiny transistor, enabling UC Irvine scientists to discover exactly how it destroys dangerous bacteria. The research could prove critical to long-term work aimed at diagnosing cancers and other illnesses in their very early stages.

Ever since Nobel laureate Alexander Fleming found that human tears contain antiseptic proteins called lysozymes about a century ago, scientists have tried to solve the mystery of how they could relentlessly wipe out far larger bacteria. It turns out that lysozymes have jaws that latch on and chomp through rows of cell walls like someone hungrily devouring an ear of corn.

“Those jaws chew apart the walls of the bacteria that are trying to get into your eyes and infect them,” said molecular biologist and chemistry professor Gregory Weiss, who co-led the project with associate professor of physics & astronomy Philip Collins.

The researchers decoded the protein’s behavior by building one of the world’s smallest transistors – 25 times smaller than similar circuitry in laptop computers or smartphones. Individual lysozymes were glued to the live wire, and their eating activities were monitored.

“Our circuits are molecule-sized microphones,” Collins said. “It’s just like a stethoscope listening to your heart, except we’re listening to a single molecule of protein.”

It took years for the UCI scientists to assemble the transistor and attach single-molecule teardrop proteins. The scientists hope the same novel technology can be used to detect cancerous molecules. It could take a decade to figure out but would be well worth it, said Weiss, who lost his father to lung cancer.

“If we can detect single molecules associated with cancer, then that means we’d be able to detect it very, very early,” Weiss said. “That would be very exciting, because we know that if we treat cancer early, it will be much more successful, patients will be cured much faster, and costs will be much less.”

The project was sponsored by the National Cancer Institute and the National Science Foundation. Co-authors of the Science paper are Yongki Choi, Issa Moody, Patrick Sims, Steven Hunt, Brad Corso and Israel Perez.

Related: full press releaseWhy ‘Licking Your Wounds’ WorksHow Bleach Kills BacteriaAlgorithmic Self-Assembly

Encouraging Curiosity in Kids

How do you help make your children scientifically literate? I think the biggest thing you can do is encourage curiosity.

One way to encourage curiosity it is by answering their questions (and not saying: I am too busy, don’t bother me, don’t ask me?, stop asking why…). I know adults are busy and have all sorts of stuff we are trying to get done; and the question about why I need to wash my hands doesn’t seem worth answering. But I think anytime a kid is asking why is an opportunity to teach and encourage them to keep being curious.

It is very easy to shut off this curiosity, in our society anyway (we do it to the vast majority of people). The biggest difference I see between adults and kids is not maturity or responsibility but curiosity (or lack thereof in adults) and joy (versus adults who seem to be on valium all the time – maybe they are).

As they grow up kids will have lots of science and technology questions that you don’t know the answers to. If you want them to be curious and knowledgeable, put in the effort to find answers with them. You have to help them find the answers in a way that doesn’t turn them off. If you just say – go look it up yourself (which really they can do), maybe the 2% that are going to become scientists will. But most kids will just give up and turn off their curiosity a little bit more (until eventually it is almost gone and they are ready to fit into the adult world). Which is very sad.

Once you get them used to thinking and looking things up they will start to do this on their own. A lot of this just requires thinking (no need to look things up – once a certain base knowledge is achieved). But you need to set that pattern. And it would help if you were curious, thought and learned yourself.

Photo of kids intently studying on a Malaysian beach

My mom with a group of Malaysia kids apparently intent on learning something. I am there, but not visible in this photo. Photo by my father.

While walking in the park, see one of those things you are curious about and ask why does…? It is good to ask kids why and let them think about it and try and answer. Get them in the habit of asking why themselves. And in those cases when no-one knows, take some time and figure it out. Ask some questions (both for yourself – to guide your thinking – and to illustrate how to think about the question and figure things out). If you all can’t find an explanation yourselves, take some time to look it up. Then at dinner, tell everyone what you learned. This will be much more interesting to the kids than forcing them to elaborate on what they did today and help set the idea that curiosity is good and finding explanations is interesting.

It is fun as a kid if your parent is a scientist or engineer (my father was an engineering professor).

You often don’t notice traits about yourself. In the same what I know what red looks like to me, I figure we both see this red shirt you see the red that I do. But maybe you don’t. I tend to constantly be asking myself why. If I see something new (which is many, many times a day – unless I am trapped in some sad treadmill of sameness) I ask why is it that way and then try and answer. I think most of this goes on subconsciously or some barely conscious way. I actually had an example a few months ago when I was visiting home with my brother (who is pretty similar to me).

As we were driving, I had noticed some fairly tall poles that seemed to have really small solar panels on top. I then noticed they were space maybe 20 meters apart. Then saw that there seemed to be a asphalt path along the same line. I then decided, ok, they are probably solar panels to power a light for the path at night. Then my brother asked why are there those small solar panel on top of that pole?

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MIT Scientists Find New Drug That Could Cure Nearly Any Viral Infection

New drug could cure nearly any viral infection

The drug works by targeting a type of RNA produced only in cells that have been infected by viruses. “In theory, it should work against all viruses,” says Todd Rider, a senior staff scientist in Lincoln Laboratory‘s Chemical, Biological, and Nanoscale Technologies Group who invented the new technology.

There are a handful of drugs that combat specific viruses, such as the protease inhibitors used to control HIV infection, but these are relatively few in number and susceptible to viral resistance.

Rider drew inspiration for his therapeutic agents, dubbed DRACOs (Double-stranded RNA Activated Caspase Oligomerizers), from living cells’ own defense systems. When viruses infect a cell, they take over its cellular machinery for their own purpose — that is, creating more copies of the virus. During this process, the viruses create long strings of double-stranded RNA (dsRNA), which is not found in human or other animal cells.

As part of their natural defenses against viral infection, human cells have proteins that latch onto dsRNA, setting off a cascade of reactions that prevents the virus from replicating itself. However, many viruses can outsmart that system by blocking one of the steps further down the cascade.

Rider had the idea to combine a dsRNA-binding protein with another protein that induces cells to undergo apoptosis (programmed cell suicide) — launched, for example, when a cell determines it is en route to becoming cancerous. Therefore, when one end of the DRACO binds to dsRNA, it signals the other end of the DRACO to initiate cell suicide.

Combining those two elements is a “great idea” and a very novel approach, says Karla Kirkegaard, professor of microbiology and immunology at Stanford University. “Viruses are pretty good at developing resistance to things we try against them, but in this case, it’s hard to think of a simple path pathway to drug resistance,” she says.

Each DRACO also includes a “delivery tag,” taken from naturally occurring proteins, that allows it to cross cell membranes and enter any human or animal cell. However, if no dsRNA is present, DRACO leaves the cell unharmed.

Very cool stuff and potentially hugely beneficial. Just a reminder: this works against viruses – not bacteria (just as antibiotics do not work against viruses).

image showing the results of cultures treated with DRACO v. those not treated

Related: Science Explained: RNA Interference8 Percent of the Human Genome is Old Virus GenesVirus Engineered To Kill Deadly Brain Tumors
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The Sun is a Miasma of Incandescent Plasma

They Might be Giants once again provide an enjoyable view into the wonders of science. Previously they published the video, The Sun is a Mass of Incandescent Gas. They published an updated video, a couple years ago, which captures the best current understanding based on the scientific inquiry process: Why Does the Sun Really Shine? (The Sun is a Miasma of Incandescent Plasma).

I really do love, They Might be Giants. Even before their focus on science I enjoyed their music. But they have done wonders with all their recent work. Go Giants. Get their DVD: Here Comes Science.

Related: How Science is Unmasking the Secrets of the Sun (Science magazine, 1974)The problem with hot gas = Test it Out, Experiment by They Might Be GiantsHere Comes Science by They Might Be Giants

Their previous video, The Sun is a Mass of Incandescent Gas, Continue reading

5% of the Universe is Normal Matter, What About the Other 95%?

Dark Matters from PHD Comics on Vimeo.

Great discussion and illustration of the state of our understanding of physics, matter, dark matter and the rest of the stuff our universe has from PhD comics. What is the universe made of? 5% of it is normal matter (the stardust we are made of), 20% dark matter and the other 75% – we have no idea!

Dark Cosmos is a nice book on some of these ideas. It is 5 years old so missing some of the latest discoveries.

Related: Why do we Need Dark Energy to Explain the Observable Universe?The Mystery of Empty SpaceFriday Fun, CERN Version
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Cancer Vaccines

A reader commented on a previous post (MIT Engineers Design New Type of Nanoparticle for Vacines) asking about how vaccines can fight cancer. Preventative vaccines can build up immune response to viruses which cause cancer. So the vaccine actually works against the virus which prevents the virus from causing cancer.

The U.S. Food and Drug Administration (FDA) has approved two vaccines, Gardasil® and Cervarix®, that protect against infection by the two types of human papillomavirus (HPV) – types 16 and 18 – that cause approximately 70% of all cases of cervical cancer worldwide. At least 17 other types of HPV are responsible for the remaining 30% of cervical cancer cases. HPV types 16 and/or 18 also cause some vaginal, vulvar, anal, penile, and oropharyngeal cancers.

Many scientists believe that microbes cause or contribute to between 15% and 25% of all cancers diagnosed worldwide each year, with the percentages being lower in developed than developing countries.

Vaccines can also help stimulate the immune system to fight cancers.

B cells make antibodies, which are large secreted proteins that bind to, inactivate, and help destroy foreign invaders or abnormal cells. Most preventive vaccines, including those aimed at hepatitis B virus (HBV) and human papillomavirus (HPV), stimulate the production of antibodies that bind to specific, targeted microbes and block their ability to cause infection. Cytotoxic T cells, which are also known as killer T cells, kill infected or abnormal cells by releasing toxic chemicals or by prompting the cells to self-destruct (a process known as apoptosis).

Other types of lymphocytes and leukocytes play supporting roles to ensure that B cells and killer T cells do their jobs effectively. These supporting cells include helper T cells and dendritic cells, which help activate killer T cells and enable them to recognize specific threats.

Cancer treatment vaccines are designed to work by activating B cells and killer T cells and directing them to recognize and act against specific types of cancer. They do this by introducing one or more molecules known as antigens into the body, usually by injection. An antigen is a substance that stimulates a specific immune response. An antigen can be a protein or another type of molecule found on the surface of or inside a cell.

Related: National Cancer Institute (USA)Nanoparticles With Scorpion Venom Slow Cancer SpreadUsing Bacteria to Carry Nanoparticles Into CellsGlobal Cancer Deaths to Double by 2030
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Gravity and the Scientific Method

One of the topics I return to repeatedly is the scientific method – theories must to tested. As evidence mounts that new ideas do a good job of explaining theories they become more accepted. But they continue to be tested in new ways as the ideas are extended and ramification are explored. And science progress means that old conventions can be overturned as new evidence is gathered.

Science is not about current beliefs. Science is about seeking knowledge. If the search for knowledge leads to evidence that old ideas were wrong those ideas are overturned. Since people are involved that process isn’t as clean as it sounds above. People get comfortable with beliefs. They build careers on expanding those beliefs. Most are uncomfortable when they are challenged and don’t accept new ideas even when the evidence mounts. But some do accept the new ideas. Some challenge the new ideas by running experiments. And some of those prove the new ideas faulty. Some become convinced of the new ideas as the results of their experiments make the new ideas seem more sensible (instead of getting the results they expected).

Building the body of scientific knowledge is not nearly as clean and simple as most people think. It isn’t a simple process, what is the underlying truth can be debatable. But the beauty of the scientific process is how it helps us overcome our biases and provide evidence to support the theories we support. The scientific method (combined with our human involvement) doesn’t mean new ideas are accepted easily but it does mean new ideas compete on the basis of evidence not just the power of those that hold the beliefs.

Is gravity not actually a force? Forcing theory to meet experiments
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Ten Things Everyone Should Know About Science

As the writer of this blog (which is located at engineering.curiouscatblog.net) I am a strong believer in the importance of scientific literacy. Neil Degrasse Tyson stated the importance very well, as I mentioned in a previous post, the scientifically literate see a different world

If you are scientifically literate the world looks very different to you. Its not just a lot of mysterious things happening. There is a lot we understand out there. And that understanding empowers you to, first, not be taken advantage of by others who do understand it. And second there are issues that confront society that have science as their foundation. If you are scientifically illiterate, in a way, you are disenfranchising yourself from the democratic process, and you don’t even know it.

The Financial Times has complied a list of the 10 things everyone should know about science

  1. Evolution – previous posts: Evolution is Fundamental to Scienceposts tagged: evolution
  2. Genes and DNA – tags: genesgeneticsDNARNA
  3. Big bang – tags: physics, posts mentioning big bang
  4. Relativity – General Relativity Einstein/Essen Anniversary Test – posts mentioning relativity
  5. Quantum mechanics – Quantum Mechanics Made Relatively Simple Podcasts, Quantum mechanics
  6. Radiation
  7. Atoms and nuclear reactions
  8. Molecules and chemical reactions – posts on chemistry
  9. Digital data – I must admit, even reading their comments, I don’t understand what they are thinking here. There certainly is a great deal of digital data and the future certainly going to involve a great deal more, but this just doesn’t fit, in my opinion.
  10. Statistical significance – Seeing Patterns Where None Exists, Statistics Insights for Scientists and Engineers, Correlation is Not Causation post on statisticsexperimentation

It is a challenge to create such a list. I agree with most of what they have. I would like to look at changing the last 2 and radiation, though. I would probably include something about the scientific method rather than statistical significance. Another area I would consider is something about bacteria and/or viruses. You can maybe include them under genes, but viruses and bacteria are amazing in the very strange things they do with genes and I think that is worthy of its own item. Another possibility is thinking of separating out a second spot for things related to the scientific method – causation, randomized testing, multivariate experiments… I would also consider one, or more of the following or something related to them biology – chlorophyll, the the life of bacteria in our bodies, something related to human health (how drugs work, medical studies…), etc..

The Ten Things Everyone Should Know About Science

Evolution through natural selection remains as valid today as it was 150 years ago when expressed with great elegance by Charles Darwin in The Origin of Species. The mechanism of evolution depends on the fact that tiny hereditable changes take place the whole time in all organisms, from microbes to people.

An important feature of Darwinian evolution is that it operates at the level of the individual. There is no mechanism for natural selection to change the species as a whole, other than through the accumulation of changes that lead to the survival of the fittest individuals.

The rate of evolution varies enormously between different types of organism and different environmental circumstances. It can proceed very quickly when the pressure is great, as, for example, with bacteria exposed to antibiotics, when drug-resistant mutations may arise and spread through the bacterial population within months.

Why does it matter? Evolution is coming under renewed assault, particularly in the US, from fundamentalist Christians who want creationism to be taught in schools. Although evolution has had virtually unanimous support from professional scientists for at least a century, polls show that American public opinion still favours creationism.

Related: Poor Results on Evolution and Big Bang Questions Omitted From NSF ReportNearly Half of Adults in the USA Don’t Know How Long it Takes the Earth to Circle the SunScience Knowledge Quiz

Naturally Curious Children

I write this blog because when I was a kid I was curious and had parents who gave me enough interesting answers and interesting resources to build on that curiosity. And I am still curious today. I love learning. And I love to hear about kids learning.

The Big Girl has worked out evolution

She was ecstatic when we ended up with a rooster in our ‘sexed’ chickens even though Mummy and Daddy weren’t too impressed, because she wants more little fluffy chicks. I think that counts as evidence she knows you need boys and girls to get babies.

“What would happen if there were no boys?” This is the question she came out with the other day.

“Well, there would be no babies.” I didn’t quite get the problem seeing we were feeding the rather prolific guinea pigs at the time and we’ve been talking about separating them.
“But what if there were no boys at all? So no-one could have babies?”
“Eventually, they would all die.”
“But there wouldn’t be any left!”
“No, they would die out.”

“How did humans start?”… a puzzled little crease in her forehead. “Because if there weren’t any around with the dinosaurs they must have started sometime. How could there be no humans and then they’re there? What was the Mummy?”

“Well, they weren’t sudden. You know how you are a little bit different to Mummy and Daddy? That’s how it happened. The babies were just a little bit different to their parents and over a really, really long time they became people.”

“But if there was only one it would die out.”
Well that came out of nowhere, did I miss half of this conversation?
“You know, the first person. It needs to have both a boy and a girl to have more people babies. So if there was only one it would die out.”
“Oh, from yesterday. Yes, you’re right. But people live in groups, so they’re all changing a tiny little bit at the same time.”

It is great to see developing minds at work. Exploring their natural curiosity. And taking in new information puzzling it out over time and then coming back to the ideas. This kind of curiosity is what drives learning and success.

Related: Playing Dice and Children’s NumeracySarah, aged 3, Learns About SoapLetting Children Learn, Hole in the Wall ComputersIllusion of Explanatory Depth

Driver Thanks Engineer Who Hit Him on Purpose

Driver thanks man who hit him on purpose

Driving to a Mariners game, Duane Innes saw a pickup ahead of him drift across lanes of traffic, sideswipe a concrete barrier and continue forward on the inside shoulder at about 40 mph. A manager of Boeing’s F22 fighter-jet program [and engineer by training], Innes dodged the truck, then looked back to see that the driver was slumped over the wheel. He knew a busy intersection was just ahead, and he had to act fast.

“Basic physics: If I could get in front of him and let him hit me, the delta difference in speed would just be a few miles an hour, and we could slow down together,” Innes explained. So he pulled in front of the pickup, allowed it to rear-end his minivan and brought both vehicles safely to a stop in the pull-off lane.

Some might say the driver of the truck, 80-year-old Bill Pace, of Bellevue, and anyone Pace’s truck might have slammed into had luck on their side that day. A retiree who volunteers for Special Olympics and organizes food drives, Pace didn’t know it at the time, but he’d had a minor heart attack two days earlier and his circulation was so poor he passed out at the wheel with his foot resting on the accelerator.

Nice story and nice that the article had a tiny bit of science in the story, with another example of good work by an engineer.

Related: Nikola Tesla, A Scientist and EngineerWhat is an Engineer?Statistics Insights for Scientists and EngineersInspirational Engineer

Science and Optical Illusions

illusion with color tiles on a cubeMore illusions by R Beau Lotto, lecturer in neuroscience, University College London

The middle tiles on the cube both have the same color, even though they appear very different to most of us.

The science of optical illusions

the two physically identical tiles do indeed now look very different.

Why? The information in the image strongly suggests that the dark brown tile on the top now means a poorly reflective surface under bright light, whereas the bright orange one at the side means a highly reflective surface in shadow.
… [from another illusion]
So why do they look so different? Because your brain takes the image on the retina and creates what it sees according to what the information would have meant in the brain’s past experience of interacting with the world.

In this case the angles suggest depth and perspective and the brain believes the green table is longer than it is while the red table appears squarer.

The beautiful thing about illusions is they make us realise things are never what they seem, and that our experiences of the world shape our understanding of it.

Studying illusions can teach us several things. We can learn that it is easy for our senses to be fooled. We can learn about how the brain works. We can also learn how to take into account how our brain works to try and adjust our opinions (to be careful we are not just interpreting things incorrectly). It is amazing to see some of the wild guidance our brains give us. Normally they do a fantastic job of guiding us through our day but they have weaknesses that can lead us to mistaken conclusions.

Related: Albert Einstein, Marylin Monroe Hybrid ImageWhy Does the Moon Appear Larger on the Horizon?Illusions, Optical and OtherSeeing Patterns Where None Exists

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