Four Diatom Problems

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(By Michael Zheng, 2015)

TEM (Transmission Electron Microscopy) is a rare skill. I did a little when I wrote:
  • Bender, R., Bellman, S.H. and Gordon, R. (1970) ART and the ribosome: a preliminary report on the three-dimensional structure of individual ribosomes determined by an Algebraic Reconstruction Technique. J. Theor. Biol. 29, 483-488.

and learned to appreciate those who do it well.

There are 4 diatom problems I’d like to see solved, for which TEM may prove critical:
  1. What is the pathway (literally, not just biochemically) by which oil droplets are formed, coalesced, accumulated, passed out of the plastids, occupy huge volumes inside the diatom, and via milking or spontaneously get outside the diatom? Such knowledge may prove critical to biofuel production.
  2. Triangular Archaea and triangular centric diatoms sometimes have square (90deg) corners instead of the “expected” 60deg. This suggests some structure, something like a centriole, in those corners. What is there, if anything?
  3. Is there any correlation between the 3D array of microtubules and microfilaments and the shape of a diatom valve? If yes, can we observe how the relationship changes during valve morphogenesis?
  4. In motile pennate diatoms, what is the pathway by which raphe fibrils are formed and exit the cell membrane? Once out, are they attached to the membrane or not, while they traverse the raphe?
Regarding #2: While most plants do not have centrosomes, diatoms do, if not proper centrioles:

Nuns work to save axolotls from extinction.

Gill, V. (2018).

Meet the nuns helping save a sacred species from extinction.

which is a ray of hope for preservation from extinction for our favorite model animal, the axolotl (Ambystoma mexicanum, a neotenic salamander).

When I “retired” in 2011, Natalie and I delivered our axolotl colony to the dinosaur museum in Drumheller, Alberta. See:

Alberta, Canada ~ Royal Tyrrell Museum of Palaeontology

Our book Embryogenesis Explained is based on our axolotl research. Susan Crawford-Young is carrying this on, and soon hopes to be imaging axolotl embryos in 4D at the Canadian Light Source (a synchrotron in Saskatoon, SK, Canada).

Visual projection to the skin in the mimic octopus? (OCTM)

I send out weekly schedules to my various collaborators and devote Mondays to taking time to speaking via Skype with anyone who might want to talk with me. I started to take the opportunity of these weekly schedule updates to let everyone know some of the ideas on my mind, of which they might want to partake. I now extend the invitation to readers of the blog. Perhaps inspired by the work of Helmut Hirsch on kitten visual cortex and the model we published in which linear receptive fields act like rays in computed tomography:

Gordon, R. and Hirsch, H.V.B. (1977) Vision begins with direct reconstruction of the retinal image, how the brain sees and stores pictures. In:  Gegenstrom, Für Helmut Hirsch zum Siebzigsten/Against the Stream, for Helmut Hirsch on His 70th Birthday. H. Schallenberger and H. Schrey, (eds.) Peter Hammer Verlag GmbH, Wuppertal: pp. 201-214.

I started thinking about the reverse process of vision. How could we get an image in our mind out, so others could see it. Now, of course, this is precisely what a fine artist does, and what happens when a forensic artist reconstructs a face you’ve seen through a set of questions. But could each of us do it ourselves, with less training, and faster? Sometime in the mid-1970s I conceived of a device that could pick up an image from our skin, by noting that each hair has a ring muscle around it. This then got the silly name of “goose bump voluntary mind reader”. As is my wont, I of course did not even attempt to build such a contraption. With modern technology, I suppose it could be built.

According to Wikipedia was discovered in 1998, and apparently can mimic 15 other animals:

Since octopuses can learn quite a bit, maybe it could do even more. So the question arises whether the patterning (and mimic behavior) is built-in? If not, then this octopus perhaps can project an image in its mind onto its skin. Perhaps, indeed, we could do the same. So here’s the tentative title for a paper:
Visual projection to the skin in the mimic octopus? (OCTM)

.Mimic
Showing you what’s on my mind

 

Turtle Rescue

Saving a sea turtle.

Tumbleweeds Tumbling

We do get involved in some crazy things, no doubt about it. There was a mass turtle stranding in our area of the panhandle in Florida where we were staying. The last time this happened was in 2006. All the sea turtle people around Florida were out seeking cold stunned turtles due to the bizarre cold weather from the polar vortex. The turtle get too cold and then end up unable to move floating on the surface. Many drown when they can no longer move enough to even lift their heads up to take a breath. Some end up washed up like debris on the shore where certain death awaits. If the cold doesn’t kill them, predators or dehydration will. Any turtle that cold be found could be brought in and warmed and saved to be released when th cold spell passed.

A call went out for folks who could…

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A New Review of Embryogenesis Explained

The review is by:

Dr. Palmiro Poltronieri
Editor-in-Chief, Challenges
National Research Council of Italy,
AgroFood Department,
Institute of Sciences of Food Productions
via Monteroni km 7
73100 Lecce, Italy

“The model discussed by the authors is based on a simple, unifying idea that differentiation waves, based on cell cytoskeleton, i.e., contraction and expansion of the network of microfilaments and microtubules, is at the basis of mechano-transduction signalling, that brings transcription factors to regulate chromatin into specific cell-stage differentiation states, based on regulons, i.e., the wholeness of opened DNA regions and inaccessible DNA regions. Thus, from determination of a cell’s fate, i.e., signaling to advancement of process, to differentiation state, i.e., new transcriptional program and reprogramming of active regulons, clusters of cells thus divide, mature and form the various cell type component tissues of the developing embryo.”

And my favourite part:

“Overall, the book is a great book, documenting with images, schematic reproductions and drawings the embryo development, showing parallelisms, universal processes and the peculiarities of various vertebrates and invertebrates.”

You can read the full open access review here:

The Science Police

The Science Police

by

On highly charged issues, such as climate change and endangered species, peer review literature and public discourse are aggressively patrolled by self-appointed sheriffs in the scientific community.

A profoundly important article that describes how peer review is really done. In most fields it is not important enough to have cables denying funding because of what the public might misperceive. Still, the science police exist. People inclined to be science police tend to gravitate to positions of power such as grants committees and senior academic administrative chairs.

I wish I had a nickel for every time we wrote a grant on our waves and got back an answer that basically said, “It’s an interesting result but it goes against the prevailing wisdom and so we won’t fund you to test it”

Our system of peer review is made up of deeply sincere individuals who are so convinced they are right and others are wrong that research progress is slowed and huge amounts of money are wasted,

I once had a fellowship application for a grant turned down with the following:

“You have written an excellent application, clearly showing your methodology and goals. Your references, publication record and previous accomplishments prove you are well qualified to do this research and you have a high probability of success. The project itself is completely novel and potentially ground breaking. However because you have never published about this topic in a reputable high impact journal we cannot fund you.”

My husband has the same committee tell him in one year he was brilliant and if the work held up it was likely time for another nobel prize in embryology. In the following year the same committee rejected him saying it is a wonder he ever graduated from high school. The only thing that changed was who the chair of the committee was.

This article is long but it very clearly illustrates a phenomena first described to me by writer and naturalist Jack Rudloe (though he says he heard it from someone else.)

“You can always tell an academic by the number of knives in his or her back.”