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applied science xcience

Fix that DNA

Today I was looking at ScienceDaily.com and found 3 really exciting developments. Bound to change medicine and our lives forever. Cancer detection, full genome sequencing on a small budget and fixing the broken Fixer responsible for the bad effects of Aging.

Cancer Detection

In the early ’70s President Nixon launched the War On Cancer. While we’ve made good progress with some cancers others defy our efforts so it’s still going on.

In the news recently we heard that 2/3 of all cancers can be attributed to copy / replication errors. Random chance. You can read more about that in this NPR piece. That means 1/3 are caused by assault due to environmental (cell’s environment) factors. Like radiation (ionizing – aka nuclear or UV/Sunshine) or chemistry – smoking , drinking and the toxic effects of other things we encounter in our lives.

It tough to beat something that results from changes to any one of tens of thousands of parts. Other diseases have simpler single causes, targets and consequently treatments and cures are more readily achieved. Not Cancer.

Part of the problem is detecting it early enough for treatment to effectively head off catastrophic results later. By the time it’s progressed to a size noticeable by people there are millions of cells involved and they’ve been there a while. If the mass of cells, the tumor, gets large enough the body begins to provide a blood supply, just as if the tumorous mass is an organ. At that point the worry is that some of the cancerous cells will shed into the bloodstream through one of these blood vessels passing through the tumor and move on to other parts of the body . . . and begin new tumor sites there.  So a lot of research goes into making cancer more detectable.

Researchers have developed computer software that can tell you if cancer is present and where in the body it is from a single blood sample. It has an 80% success rate at this stage of development.

Cancer is a genetic sequence alteration in the DNA. Encapsulating the double-helix structure of the DNA is a sheath of molecules which we now know play roles in inheritance and the operation of the biological machinery of gene expression. This field is called epigenetics and the molecules involved are the epigenome.

As previously mentioned material from the tumor site will enter the blood stream. Not all that material is complete cells – some of it is just the components of cells that have broken down into fragments. In these fragments you can find molecular markers that are associated with cancers of various types. Methylation patterns specific to cancers originating in specific tissue for instance. The researchers have created a database of these chemical markers and their software uses that to compare samples against. It works best against tissues that are well circulated with blood such as the heart and lungs.

As progress is made and the techniques refined it will only get better.

Full Genome Sequencing On A Small Budget (Fast)

We’re all familiar with genome sequencing now. The Human Genome project is a decade past, DNA crops up in court cases and crime TV a lot and lately more than one company is hawking personal genomic analysis for reasons from concerns over health to curiosity about ones history.

What most people don’t know is how that works.

The Human Genome project cost Billions and took Years. It sequenced a complete genome from end to end of a specific person. This is a Reference Genome.

All the applications mentioned above don’t sequence a person’s whole genomic sequence. That would take millions of dollars and lots of time. They sequence fragments which are then either compared to a reference genome or analyzed for specific markers.

Comparison would show where one genome differs from another genome. Marker analysis looks for DNA sequences known to be associated with specific traits or maladies.

Doctors often have to treat patients that they know have something out of whack somewhere in their genome but they don’t know where. And if it’s novel or there aren’t any known markers for it then medicine is stymied as to the genetic origin.

Imagine for a minute that when you reached adulthood they took a snapshot of your genome – just like they did in the human genome project. And that was stored for later use. Later meaning when they think something is happening. At that point they take another snapshot of your genome. And then they compare the new one against your reference one, the one they took when you matured.

This comparison could show where changes have happened and that could give the doctors a better idea of what is happening and how to treat it.

Researchers have figured out a technique called 3D Assembly which brings the cost of full genome sequencing down from $4 Billion to about $10,000. And it is said to be fast, ‘amazingly fast’.

It uses knowledge about folding to trace the genome as it folds. By using this knowledge they can take hundreds of millions of short sections and assemble them to reconstruct a ‘de novo’ genome assembly. So that reference genome can be generated as required in relatively short time.

Fixing The Broken Fixer Responsible For The Bad Effects Of Aging

As our cells divide new copies of our DNA are made. Errors occur during this process resulting in DNA that is not an exact copy. Chemicals and radiation can also change our DNA. Which is why we have a mechanism for repairing our DNA.

But as we get older this repair mechanism becomes less and less effective. And more and more malformed DNA, mutations, accumulate. Leading to cancer and cell malfunction. This is one of the major processes of ageing.

Well researchers have figured out which processes are affecting which materials and how to ‘fix’ that. And in mice they’re reversing the effects of ageing!

In the mice they can see positive indications of restored DNA repair function. These mice also show less damage due t radiation exposure than would normally be the case.

It’s just a matter of time now before we get to a place where we don’t have to suffer while getting old.

I was sure that I’d heard that Timothy Leary said “There are people alive today that will never die . . .” and when I did a quick Google search I came across a link to a book I’d read in Google Books. In the page this links to I read that a number of polls of life extension researchers put the point at which life extension melds into immortality sometime in the 21st century. One of the polls in 1969 had a spectrum of predictions ranging from 1993 to 2017 . . . who says predictions of scientific progress have to be wrong 🙂

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Role Playing Leads to Mixed Up Players

Recently a report was published about the work environment in the Vancouver School Board. You can read about that in this CBC article. The report was prepared for WorkSafeBC (the workers compensation board’s current incarnation)

Last fall the VSB trustees were fired by the provincial government for various other reasons. There was talk that the work environment in the office had become toxic with Board Trustees being bullying and abusive towards staff.

The report just published lays this out and confirms these allegations.

In yesterday’s newspaper an article appeared that says a number of Unions have come together to issue a statement denying the report. At least one of these unions is CUPE, the Canadian Union of Public Employees. That’s the union I’m in with my job. All of us who work in the office there are CUPE members. I’m assuming that the staff in the VSB offices were also Union members. Likely CUPE members.

So why would all these unions come out on what would appear to be a Management side?

Well it turns out that Unions had representation on the Board of Trustees. So along with the elected Trustees there were Union members sitting at the same table.

And the report apparently said that these Union members of these committees were just as culpable in the bullying as others. The Unions say no they weren’t. They say the process was faulty and likely politically motivated.

I’m curious what the staff members in the VSB office would say. I’m assuming that one aspect of preparing the report was to interview them so I’m guessing that they told the outside consultant of anecdotes which entailed abuse and bullying.

This wouldn’t be the first time a Union has been accused of not being able to properly manage its office workers. At some point in the late 1990s workers at a union office in the Vancouver area threatened strike if memory serves me. I’d imagine stories like that come out in other places where Unions have offices large enough to have paid staff.

So how does this happen?

A short while ago I ran into a study which showed that simply putting on a police uniform changes your attitude towards specific groups. In the study they found that just putting on a uniform caused participants to exhibit a bias again a visually identifiable sub-group. What was a bit unexpected was that sub-group. Many assumed it would be people of colour but it turned out to be people in hoodies.

People in hoodies have become synonymous with poor, angry, disenfranchised people that tend to hold violent protests in groups. Or engage in illegal activities as individuals. It’s not that putting on a hoody turns you into a criminal, it’s the media reporting and presentation of these groups and individuals fitting into them that has resulted in this perception.

So that gets reflected in the unconscious behaviour exhibited by those in the study who put on the uniform of the police.

How does this relate to the story at the start?

Well if your employment background is steeped in the culture of Management vs Labour and White Hats vs Blue Hats then you see those seats at the committee table in one way: Those are managers sitting there. Even if your background is labour, when you take that seat it’s like putting on that uniform: you have a role to play, and it’s not a labour role.

So when the staff (workers) tell you (manager) that your ideas and requests cannot be dealt with because they are incorrect there might be a tendency to see them (workers) as not following (management) commands. Any repetition of this could be seen, and felt, as obstructionism. And from the staff’s perspective a boss is a boss is a boss . . .

So playing the roles on a totally subconscious level you get union-managers treating union-workers the way that managers treat workers. And workers responding the way that workers respond to managers.

I would submit that it would be really difficult for people on either side of that transaction, in that environment, to behave any other way. They are only human after all.

It’s too bad we either refuse to recognize that or own up to it.