Exploring Brooklyn in Pictures

A couple days ago we explored Brooklyn. We first took the subway to the City Hall stop in Manhattan (the best for walking the Bridge toward Brooklyn) and then walked across the Brooklyn Bridge. It’s about 1.2 miles and a fun walk, although on our walk it was about 90 degrees and humid. Nice breeze in the middle, which helped.

We then explored the Dumbo area of Brooklyn, had pizza at the famous Juliana’s Pizza (run by the Grimaldi family who sold the business Grimaldi’s and then the two businesses kind of swapped places). Best pizza I’ve ever had, but waiting in line was tough in the blazing sun. We went to the Brooklyn Flea Market and bought some vintage stuff. Had ice cream at the Brooklyn Ice Cream Factory, and then took the subway back.

Below are a bunch of pictures from our day in Brooklyn.

Juliana's pizza Brooklyn

Juliana’s pizza Brooklyn

Brooklyn sign

Brooklyn picture

Brooklyn architecture

Brooklyn Bridge from Brooklyn

Manhattan Bridge from Brooklyn

Brooklyn factory shutters

Brooklyn factory shutters

Brooklyn Bridge Statue of Liberty

Brooklyn Bridge

Brooklyn Bridge

Scientist in the Garden: lessons for stem cells & science

Here’s another edition of my posts over the years in my series ‘The Scientist in the Garden’.

Can gardening teach us some important things about stem cells and about doing science more generally?

Regular readers of this blog know that I am really into gardening and especially during the last 5 or so years I’ve been growing many kinds of unusual tomatoes. They like it here in the Sacramento region a lot more than they did in my previous city of Seattle, WA. This year I’ve planted more types of tomatoes than ever.

It’s probably not surprising to you that I see parallels as someone who is really into stem cells and into gardening.

tomatoes Sacramento

One plate of more than 50 lbs of tomatoes grown in the Knoepfler garden in 2016

Know your seeds and cells. If you think of stem cells as akin to seeds, what goes on in the tomato garden has some lessons for the stem cell and regenerative medicine field. For instance, the source of stem cells makes all the difference and the same goes for seeds and plants. I have planted either seeds or plants in the past only to find a few times that they weren’t what the place who provided them said they were. The lesson there for the lab is “know your stem cells” and validate them. They might not be what you think….even if you yourself established them they can drift or get contaminated. We need to pay close attention. It’s odd to expect a yellow tomato and have a red one grow, but it’s much worse to think you are using one type of stem cells for your paper or your clinical trial only to find it wasn’t what you thought. Also, if a plant or seeds or cells are struggling, it’s probably better to start over (see more below on stuff will go wrong) rather than try to rescue something that isn’t working.

The bed and niche can make all the difference. The last few years I’ve been putting energy into improving the soil in my garden beds by growing cover crops, adding mulch, and even adding worms. If you think of a garden bed and its soil, sun, etc. as a plant niche akin to the stem cell niche, both have big impact for better or worse.

Stuff will go wrong. Expect setbacks and problems. Last year in my tomato garden there were two problems. One was rampant slime molds, most likely from some wood chips I used as part of my compost. I had to change how I watered and mostly I got things under control. Roly-poly bugs even ate some of the slime mold (see below). Gross but interesting, right? Then there was the leaf-footed bug invasion. This year it is, perhaps due to the wet winter or the past year’s slime molds, a population explosion of roly-poly bugs in the Armadillidiidae family, those funny terrestrial crustaceans of the garden. I’ll do a future post on how I tackled this 2017 garden problem.roly-poly slime mold

Apparently in the Sacramento region a little slime mold in the garden isn’t uncommon, but it becomes a problem if it is all over the garden beds and when it dries it gives off spores that are probably not great to breathe. Same
with roly-poly bugs. In moderation they are helpers in the garden by recycling old plant waste as they’ll eat just about anything even slime mold, but if they show up in the 1000s in one area then some of them start eating living plants like happened with my cucumber and tomatillo plants.

You can expect occasional problems in the lab with your stem cells too. Maybe the cultures get contaminated. Maybe they stop growing. Don’t panic. Think it through and try some different solutions. When in doubt, start anew with fresh cells and media. This is where when it comes to stem cells having a large, dedicated bank of early passage cells is crucial so that you can go back to them and start from the beginning.

Patience. I’m not a super patient person, but gardening and science both demand patience. The fun I’m having now watching my big tomato plants growing, setting fruit, and some even ripening (we’ve eaten four small tomatoes so far)  all began a long time ago. As I mentioned above, I put work into the soil and planning. I even keep notes from past years’ of gardening and refer to them. I haven’t yet grown tomatoes much from seed so I use seedlings and someone started those probably months before I planted them. It’s the same with stem cells and other kinds of experiments. Sure we all are understandably in a hurry to publish, get data for grants, and so forth, but also keep an eye on the big picture and try having a certain patience for science.

If you are a scientist and you’ve never gardened, you should give it a try. I bet you’ll see the parallels and unlike most science, you can eat the results. It can even be as simple as a couple potted tomatoes or one small wooden planter.

Bioquark “reawaken” the dead with stem cells plan just zombie fodder?

A company called Bioquark reportedly claims it intends to bring back the dead, as in deceased people or at least brain dead people, with stem cells. Or at least awaken their brains. If it works, would those people be like zombies? Is it ethical to experiment in this way on dead people?

We first met Bioquark last year when their “reanima” idea got some media buzz and I blogged about my skepticism here. From my 2016 post:

“The idea seems to be that injection of stem cells into the brain stem could lead to enough rejuvenation to reverse brain death at least partially and this would be done in combination with laser stimulation of the brain. I need to learn more, but how exactly could lasers affect the brain positively? More broadly, I’m skeptical of this approach.”

Fast forward to today. Apparently things didn’t work out in India with the plans for reanimation of the dead via stem cells plan as the Daily Mail reports it was “shut down”. I guess the plan now has shifted geographically to Latin America for a “trial”:

“And now, CEO Ira Pastor has revealed they will soon be testing an unprecedented stem cell method on patients in an unidentified country in Latin America, confirming the details in the next few months.

To be declared officially dead in the majority of countries, you have to experience complete and irreversible loss of brain function, or ‘brain death’.

According to Pastor, Bioquark has developed a series of injections that can reboot the brain – and they plan to try it out on humans this year.

They have no plans to test on animals first.”

There may be real effects of laser stimulation on the brain and I’m certainly convinced that stem cells have great potential for CNS conditions, but this Bioquark effort seems way out in left field (of the cemetery) in my opinion.

Some may ask, “if a brain-dead person’s body is otherwise healthy and if you could somehow heal part of their brain enough to regain consciousness or even just a more active brain, might that be a good thing?” In theory “maybe”, but in practice almost certainly not as there’s likely a medical reason his or her brain is dead in the first place such as profound brain damage. Others might ask, “Isn’t experimenting on dead people OK?” It’s different than doing clinical studies on living people of course, but just because someone is brain dead doesn’t mean you have carte blanche to do whatever. There are ethical issues and guidelines still.

And no animal testing first? That’s a big red flag, if accurately reported by the Daily Mail.

If you had strong pre-clinical data from animals that proved there was something to this hypothesis in the first place then maybe that is a place to start discussions even if not clinical experiments.

Bottom line. In my opinion this kind of research isn’t a very good idea. Instead, in the neurological arena it makes more sense to focus energy, resources, and time on using stem cells to try to have a regenerative effect in the nervous system of fully living people who are suffering from neurological disorders. There are promising trials in this area on living patients based on concrete data.

How do you rate Trump on science so far?