Category Archives: Nerdy Tumbleweeds

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

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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: