Author Archives: tumbleweedstumbling

About tumbleweedstumbling

I have three blogs, embryogenesis explained, tumbleweed tumbling AND fulltimetumbleweed. I am a retired scientist, and my husband and I have written a book which was published by World Scientific Publishing in Nov 2016 called Embryogensis Explained. Full time tumbleweed was my first blog which I worked on during five years of living full time in a travel trailer. I have now retired that blog in favour of Tumbleweeds Tumbling since we bought a stick house in April 2015 and are no longer full-time. I have a blended family of five sons and one daughter, all grown up now. I am (step)grandmother to nine boys and one girl. My husband and I have a dog and a cat. We live in Manitoba, Canada, in a 480 square foot house on a half acre of land in the tiny town of Alonsa.

Must read article: Climate Change Models Just Don’t Work.

This critically important paper proves with careful analysis something I have suspected for years. Climate change models don’t work. They don’t predict anything. They aren’t of any use for anything. Now what is needed from all scientists is some very serious and open debate on this topic. That goes double for those in any scientific organization that endorsed Climate Change. Prove Dr. Frank wrong. I don’t think it’s possible.

Open access that can be read here.

Lay summary by the author here.

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The Differentiation Code.

Our newest embryology related publication is now out. It is especially nice to get this out given the scare we got last June.

The Differentiation Code

Richard Gordon, Natalie K Gordon

Abstract

In code biology we seek a presumably arbitrary, and thus symbolic relationship between two or more entities, such as the relationship of the DNA triplet code to amino acids. Here we review the differentiation code from the code biology point of view. We observe that lineage trees of mosaic organisms can be subsumed as special cases of differentiation trees of regulating embryos. The latter can be empirically discovered as a bifurcating tree of contraction and expansion differentiation waves that recursively divide the embryo into its cell types. A binary digit, 0 or 1, assigned to each wave results in a binary number corresponding to each cell type, and may be called the differentiation code for that cell type. The differentiation tree has a correspondence in the genome, in terms of the genome’s logical structure. For a given cell type, the path to it from the zygote is marked epigenetically on the genome. Thus the differentiation code symbolically maps an epigenetically marked subset of the logical structure of the genome to the phenotype of a particular cell type. The waves involved and signal transduction from the cell state splitter to the genome are intermediaries in this relationship, and may also be arbitrary choices, and thus part of the code. In full, differentiation code = history along the differentiation tree of the differentiation wave types leading to a given cell type ⇔ contraction or expansion of the cell’s cell state splitter ⇔ activation of one of two signal transduction pathways from the cell state splitter to the nucleus ⇔ activation of one of two readied gene cascades (the “nuclear state splitter”) ⇔ epigenetic marking of the selected portion of the logical path. Each wave is in effect a cybernetic control system that results in differentiation of a set of cells and initiation of two new waves (cybernetic systems) as its goals. The differentiation code forms a basis for open evolution and its appearance was one of the major evolutionary transitions.

The Scare

Tumbleweeds Tumbling

My husband had a headache. He took a nap and woke up an hour and a half later and couldn’t move his arm properly. Next thing he’s being transferred from our small rural hospital to a major teaching hospital with lights, sirens and a full stroke protocol organized.

IMG_1707 (1)

We got lucky. Hubby dearest had a dissection of the inner carotid artery causing a mild stroke. He had four days in hospital and was released with residual damage only the neurologist can detect. It was the mildest stroke one could have. The neurologist also said all the signs the stroke occurred should vanish completely because it was so very mild. If one has to have a stroke, this is the type to have.

The dissection is considered traumatic in origin because of a seatbelt accident. That means it will likely not happen again. All the other blood vessels are clear with…

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Axolotl salamanders provide clues to spinal cord regeneration

I was really upset when I heard that Superman, Christopher Reeve, was injured in a riding accident resulting in a severe spinal cord injury. Complications from the injury eventually caused his untimely death. When the Reeve Foundation was formed I contacted them and spoke at length with someone in the new organization about what the axolotl could do. It was a song I continued to sing over and over again to anyone who would listen. I would like to think someone did listen. Still it’s so obvious to anyone who knows anything about the near miraculous ability of the axolotl to regenerate that understanding this would lead to many regenerative breakthroughs that I realistically can’t take any credit. It would appear a huge step has been taken in that possibility.

superman-curse

This is a fascinating article on why the axolotl can regenerate the spinal cord after an injury but humans cannot. These scientists have located the precise master gene involved and the exact differentiation tree pathway accessed by the axolotl. In humans, this activation does not happen because a scarring pathway is activated instead. If the genes for the regeneration pathway are still intact in humans, we now have the potential to stimulate the cells at the site of a spinal cord injury so they go down a regeneration pathway to regenerate the spinal cord instead of scarring and destruction.

If this works the potential is endless. Axolotls can regenerate their hearts, their limbs, and even their brains. Imagine those who have lost a limb now being able to grow a new one or someone in heart failure just growing a new heart. The possibilities are endless.

This discovery also happens to fit our model in Embryogenesis Explained.

Original article:

AP-1cFos/JunB/miR-200a regulate the pro-regenerative glial cell response during axolotl spinal cord regeneration

Nice summary/explanation

Axolotl salamanders provide clues to spinal cord regeneration

 

Alonsa Tornado Part One – Our own near miss.

We had a near miss with a tornado Friday August 3, 2018. We are fine. it was close but we did not suffer any damage at our home.

Tumbleweeds Tumbling

It began while we were sitting outside enjoying the cool breeze in the heavy damp heat we had been experiencing. We could hear a storm forming up to the southwest but there nothing awful was on radar so I wasn’t worried.

Tornado

I would later learn the storm formed outside of radar range because the Fox Warren is down for renovations and that leaves a blind spot right where this storm was. I could tell we were going to get a bad storm so we moved the truck into the garage. There was a lot of thunder and it had that “hail is coming” look you get to know on living on the prairie. We moved back inside and were soon absorbed in our writing.

It was our dog Misty barking that first caught my attention again. I was writing and she leaped up and barked her full dog alert at…

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Four Diatom Problems

Zheng2015 Late Fig 43782_MediaPlayer_63659_06222015_195640

(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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