061: New Blood Test for Cancer, and so much more!

Coming up on this week's show

The Climate Lounge with Tom Di Liberto

Science News:

  • Cancer Blood Test “Enormously Exciting”
  • Maths Strikes a Blow for Democracy
  • Sea Snake Found Off California – How'd It Get There?
  • Science After a Year of President Trump

Science News with Sophie McManus and JD Goodwin

Cancer blood test ‘enormously exciting’

Big story – a new blood, cheap test that could detect different types of cancer. I found out about this from BBC news, but the research is published in Science. The scientists’ vision is an exciting one – a readily available annual test for common cancers.

The work was done at Johns Hopkins. The test could detect eight common cancers. What’s new about this test, CancerSEEK, is that it detects both DNA and protein. Let’s have a quick background on cell biology and cancer.

So our genetic information is coded by DNA, packaged into genes, in all the different cells of our body. Generally speaking, our DNA enables our cells to make different proteins, that allow the many different types of cell to do their jobs. For example, our skin cells make different proteins that give skin its properties – elasticity and so on. Certain cells of the heart make contractile proteins that allow the heart as a whole to pump and keep us alive. There are hundreds of specialised cells in the body, which normally fulfil exquisitely specialised tasks. In cancer, mutations arise in our DNA. Mutations can be caused by the environment (for example, by smoking, or exposure to other cancer-causing agents in our environment), or can be inherited, or they can just occur spontaneously as our cells divide in a process of natural turnover. For example, our skin cells don’t live long – they are constantly dividing so we have nice new skin. The division process is incredibly accurate most of the time, but sometimes there are mistakes that aren’t corrected in the DNA. If this happens, cells can divide in a less controlled fashion, forming a growth – a tumour, of which there are many, many different types. These copying errors occur by chance. This is why cancer is more common as we age, as we accumulate various mutations, increasing our risk of tumour formation.

Tumours form for various different reasons, in various different tissue types. Once formed, they shed bits of their mutated DNA and proteins into the blood. This CancerSEEK test, as I said, takes blood from the patient and assesses for the presence of mutations in 16 genes that regularly arise in cancer as well as eight proteins that are often released from tumours. In the 1005 patients with clinically detected cancers in the study (a case-control study), the test detected 70% of the cancers.

A crucial step in improving patient outcomes is earlier detection of a cancer. This test would hopefully improve the diagnosis time for common and deadly cancers. For example, pancreatic cancer has very poor survival rates, in part because it often has few noticeable symptoms, so is typically detected at a late stage, when the disease is really established and harder to tackle. Of the eight cancers present in the patients of the study, five currently have no early detection programme.

Lead author Dr Cristian Tomasetti, from Johns Hopkins University School of Medicine, told the BBC: “I think this can have an enormous impact on cancer mortality,” because if tumours could be detected earlier, when they are easier to surgically remove or treat with chemotherapy, the life expectancy of the patient will probably be improved. Dr Gert Attard, team leader in the Centre for Evolution and Cancer at the Institute of Cancer Research, London, and consultant medical oncologist at the Royal Marsden NHS Foundation Trust, told the BBC: “This is of massive potential’ and compared the test to a Holy Grail for cancer treatment.

The test is now being trialled in patients who have not received cancer diagnoses, to help verify whether it could actually be useful in early detection. If so, then Cancer Research UK say that it could be used as a tool within five or so years.

As ever, there are caveats – in the case of some cancers, for example prostate cancers, the treatment may be a worse option for the patient than just monitoring the tumour, if it slow-growing and unlikely to worsen. Another point to make is that this trial was looking at clinically diagnosed cancers, the successful detection rate for early stage cancers in the sample group was 40% – it seemed less successful in this small study for the early cancers, and that is where the hope lies. If sensitivity for early stage cancers can be improved and shown in a larger patient group this will be probably really exciting for cancer diagnosis and treatment.

BBC News Health

 

Maths strikes a blow for democracy

This comes to us from an editorial in the 17 January issue of Nature.

Hungarian mathematician Alfred Renyi who reportedly said, “A mathematician is a machine for turning coffee into theorems”.

Earlier this month a US federal court struck down a particular method that officials in North Carolina were using to unfairly partition the state into electoral districts.

Gerrymandering, define term. Done to gain a political advantage for political parties.

Gerrymandering not illegal, within reason. Federal court cited the work of mathematicians including Jonathan Mattingly, an expert in mathematical modelling.

Three-judge court stated that the districting had unfairly favored the Republican Party.

John Mattingly used an algorithm that produced around 24,000 maps of different district configurations that were randomly drawn on the basis of geographic criteria.

He discovered that these Republican-drawn districts were gerrymandered to a greater degree than almost any one of his 24,000 maps!

His maps nearly all gave a larger number of wins to the Democratic Party and, in many cases, gave it the majority.

Previous rulings have struck down gerrymandering on issues such as racial and ethnic disparities

This ruling unique in that it struck down the districting for favoring one political party over another.

North Carolina has filed an appeal and it will likely end up in the United States Supreme Court.

Supreme Court has previously ruled against politically motivated gerrymandering, but lacked any real metrics

But thanks to mathematicians and computer simulations that may be beginning to change.

Upcoming 2020 US census will trigger widespread redrawing of electoral districts.

Nature

 

Sea Snake Found Off California—How'd It Get There?

This story source is National Geographic. The yellow-bellied sea-snake is venomous and well-travelled – ie it has the widest range of any snake on Earth. It looks like its range is expanding – most probably due to, guess what, climate change.

This month a yellow-bellied sea-snake washed up off California shores, several hundred miles out of its normal range. It was termed a poor waif! It’s rare for these snakes to get so lost. One was found in 1972, and three others in the winters of 2015 and 2016. However the other four snakes all washed up in El Nino years when ocean currents change. 2017/18 is not an El Nino year.

These snakes are interesting! They live in…the sea…and drink rainwater that lands on the surface of the water. They give birth to live young straight into the sea. Whole new relevance to the phrase ‘sink or swim’. They thrive in tropical waters, but sometimes – as in El Nino years, or this month, warm ocean currents send them the wrong way. As put by University of Florida biologist and sea snake expert Harvey B. Lillywhite, “So periodically one will show up in New Zealand, one will show up in California. What we're talking about is the appearance of an occasional waif.”

Current potentially responsible here is the Davidson current, which scoots snakes up North from Baja to California. But this only happens if the snakes have wandered far enough to hit this current – a phenomenon herpetologists such as Lillywhite are attributing to warmer global temperatures.

Upshot? For Californians, perhaps be a little bit (more) wary of a winter dip (not really). But this is definitely worse news for the snakes, as an unexpected trip to colder waters usually proves fatal. In the case of this unfortunate adventurer, biologists reached it when it was very distressed so it had to be put down.

Sorry to end on a slightly sad note…

National Geographic,

 

Science after a year of President Trump

Considering that the President will be delivering his State of the Union address at the end of the month I thought we should get some perspective on how he and his administration have been doing when it comes to science.

It’s been one year. Was our concern last year warranted or have we been pleasantly surprised?

I think you know that answer to that.

Trump has indeed lived up to our worst expectations, sometimes exceeding them.

Scientists in this country have been amazing stalwart in spite of the difficult circumstances.

And now they’re beginning to raise their voices, and in some cases are putting aside their scientific aspirations to run for political office.

Because it is quite clear that Donald Trump is bad for science, and bad for America’s role as a leader in science.

Let’s go down the list.

  • The withdrawal from the Paris climate agreement
  • Installed pro-industry leaders on science advisory boards which has resulted in unprecedented regulatory rollbacks from environmental agencies
  • The failure, the RECORD BREAKING failure to appoint a science adviser.
  • And many other science-related agency positions remain unfilled.
  • These aren’t just jobs to fill. These posts play a critical in advising the President, and his Administration as well as providing information to formulate sound science policy, formulate budgets, and legislation.
  • His administration has cut off funds to organizations abroad that promote public health, but if they mention abortion…well, the money gets cut off
  • He’s weakened restrictions under the Toxic Substances Control Act
  • How about censoring the language of government agencies from using terms such as “evidence-based” and “climate change”. This is so egregious that it just doesn’t seem real. But it’s real.
  • Advisory groups, including one on HIV and AIDS, have been disbanded
  • Scientists with Environmental Protection Agency grants have been banned from serving on the agency’s advisory boards.
  • The loss of scientific talent as a result of the travel ban on Muslims
  • Trump installed former Texas Governor Rick Perry as secretary of the Department of Energy (which Perry had once vowed to shut down).
  • Last week most of the National Park System Advisory Board resigned in protest of the administration’s policies on climate change and the environment.

There are a couple of things that Trump hasn’t done yet, but his previous actions have anyone concerned walking on eggs as it were.

For instance, little has happened to budgets at key science and health agencies…so far

And they haven’t yet banned research using fetal and embryonic stem cells

But maybe that’s only because they just haven’t gotten around to it

But not all is doom and gloom

Donald Trump has caused a groundswell of political activity by scientists that is unprecedented

…such as Hans Kierstead, a PhD neuroscientist and world-renowned Stem Cell researcher who is running for Congress in California’s 48th District.

Or volcanologist Jess Phoenix who is running for Congress in California’s 25th District

These are scientists who are taking action, and they need our support

Yes, I did leave out a lot of anti-science actions taken by this Administration.

There’s just not enough time to include them all.

It is apparent the the state of the union, when it comes to science, is poor

But we can change that.

Nature


The Climate Lounge with Tom Di Liberto

2017 was one hell of a year. Just a few things happened, so you are forgiven if you can’t remember it all. But here in the climate lounge, it’s time to “relax”, kick up your feet, and look back at some of the horrible weather and climate disasters that impacted the United States during the last year (with some global shoutouts too).

Every year since 1980, the scientists and economists at the National Oceanic and Atmospheric Administration’s National Centers for Environmental Information have looked back at the previous year to calculate the number of weather and climate events whose overall damage costs exceeded 1 billion US Dollars (adjusted using the consumer price index). Since scientists started this effort in 1980, there have been 219 events which cost over 1 billion dollars. Cumulatively, they have cost the US around 1.5 trillion dollars. And 2017…. Drumroll please.

Was the most damaging year on record for the United States. And it wasn’t even close. The year had 16 billion dollar weather disasters three tropical storms, 8 severe storm events, 2 inland flooding events, a crop freeze, drought and wildfire . This tied the previous record for separate billion dollar events set in 2011, although that is somewhat unfair since this measure counts all wildfire events in one cost. And this year, had multiple devastation wildfire events that cost over 1 billion individually (only 2003 could make that claim previously).

And the total amount of damaged slightly exceeded 306 billion dollars! This broke the previous record by 91.4 billion dollars, or said another way, a little bit more expensive then the net worth of Bill Gates. 86% of this whopping total came from hurricanes Harvey, Irma and Maria (which by the way still has left people in Puerto Rico without lights since it’s landfall in late September).  Let’s briefly look at these three events

Hurricane Harvey made landfall in Texas as a strong category 4 hurricane before stalling and dropping up to 60 inches of rain around the major metropolitan city of Houston. Over 30 inches of rain fell in a matter of days over 6.9 million people! It’s damages reached over 125 billion, the second costliest disaster to impact the US (1st is hurricane Katrina which hit New Orleans).

Hurricane Irma devastated the US Virgin Islands before riding up the spine of Florida causing massive damage amounts up to 50 billion dollars.

And then there is hurricane Maria which I have mentioned countless times before. Its damages cost around 90 billion and has left Puerto Rico in dire straits. They will be rebuilding the island for many years to come.

It was a horrible year. Looking back at history, it’s not surprising that most of the damage costs came from tropical cyclones. They have caused over half of the damage costs since 1950 but only number around ⅕ of the total events. The pure strength and widespread impacts of these events make them stand out in particular.

But these weren’t the only events this year. It was a diverse year for horrible events as if Mother Nature had an evil checklist that she was checking off. We hit most of the major categories except for a billion dollar winter storm. But to keep this short, let’s focus on one other”event”, wildfires

They cost the US around 18 billion dollars this year, 3 times as much as the previous record for wildfires. The wildfires in particular in central California were the most expensive on record and horrifically, the deadliest since the 1930s.

Did I mention it was a horrible year? This was just the US! Globally, some other horrible billion dollar events including some huge flooding in China and Peru. And other cyclones across the globe like Cyclone Debbie in Australia.

And the number of billion dollar events has been on the rise in the US. A frightening thought. The reasons are a bit varied but one of the major reasons is that there has been an increase in people and material wealth over time. Basically people and stuff are sprawled out, making it more likely a bad weather/climate event affects people and costly things. Also, we continue to live and expand into vulnerable areas (of which there are even more reasons for that). And secondly climate change. Climate change is increasing how often certain events like drought and heavy rain events occur. More events, more bad things. It’s an ugly combo that needs better strategy and planning.

Now, don’t think that every year will be a record breaker like this. There is a lot of variability from year to year just as there is variability in how many hurricanes or cyclones occur. But with more people on this planet, with wealth increases, and as we build in bad areas with insufficient building codes for weather and climate extremes, it would not be surprising to see that trend continue.

2017 Was One Hell of an Expensive Year for Weather and Climate Disasters in the USA


In Closing

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