@Bob Helm: Most of this information, in this particular article, …

Comment on Dr. Richard Lenski’s “Unicorns” by Sean Pitman.

@Bob Helm:

Most of this information, in this particular article, has already been published by others in various journals. The only thing I contributed here of any uniqueness is the concept of changes in the ratio of beneficial vs. non-beneficial sequences in sequence space at various levels of functional complexity.

When I submitted the technical argument for sequence space to Origins (a few years ago), they told me that it was too technical for their readership to understand. I should probably try again to submit a toned down version for more general readership.

Sean Pitman Also Commented

Dr. Richard Lenski’s “Unicorns”
There was no change in the citrate receptor or transport protein, or any other protein. No structural change took place at all. You simply don’t understand the Lenski experiment. All that happened was that the gene that codes for the citrate transport protein, which already existed and was active under anoxic conditions, was turned on in an oxygenated environment by being placed next to an active promotor. That’s it. There’s simply no new receptor being made here. No new gene or protein – olfactory or otherwise.


Dr. Richard Lenski’s “Unicorns”
I’ve read your blog about the Lenski experiment “Microbes: living in the past”. However, I think you’re mistaken. You wrote:

The adaptations arose [in the Lenski experiment] due to the de novo creation of olfactory receptor genes under conditions that would otherswise lead to death by starvation.

This simply isn’t true. No new receptor genes evolved at all – olfactory or otherwise. The very same genes stayed exactly the same. The only thing that changed is the location of the very same genes within the genome. Also, the bacteria were not starving. They simply started using citrate as an additional source of energy to the nutrients that they were already being provided with – over the course of the decades that Lenski has been running this particular experiment. I see no evidence for epigenetic factors in play here or thermodynamic instability before or after the changes in function.

Sean Pitman
www.DetectingDesign.com


Dr. Richard Lenski’s “Unicorns”
It doesn’t matter what stressors may or may not contribute to protein biogenesis. The fact remains that whatever else might contribute to mutagenesis, novel proteins are dependent upon novel genetic mutations. In this particular Lenski experiment, no novel protein was produced. However, there was a novel genetic mutation that gave rise to the new functional abilities of the E. coli bacteria. This genetic mutation simply allowed a protein-coding gene to be turned on in a different type of environment by moving a gene to a different location within the genome. Statistically, this isn’t a problem given the number of bacteria in the steady-state population over the course of a few tens of thousands of generations. It’s very predictable in fact – statistically. What is not statistically tenable, however, is the evolution of a qualitatively novel protein-based system of function that requires more than 1000 specifically arranged residues. Such a feat is not statistically feasible – and Lenski should know better than to suggest otherwise.


Recent Comments by Sean Pitman

The Arguments of Adventists Opposed to Vaccines
The LORD does not suffer fools who deliberately put themselves in paths of known dangers. If you deliberately jump off a cliff, putting the LORD to the test, this is not virtuous faith, but presumption – a sin against God.


The Arguments of Adventists Opposed to Vaccines
After extensive review of the available data, the FDA issued “emergency use authorization” for the Pfizer and Moderna mRNA vaccines. Pfizer, in particular, is planning on applying for full FDA approval as early as the middle of this month (April 2021).

As far as the length of immunity, it is currently known that robust immunity following mRNA vaccination lasts “at least” six months, and probably years (Link). However, if additional variants arise that aren’t effectively covered by the current vaccines, additional booster shoots would be needed.


Are mRNA Vaccines for COVID-19 helpful or harmful?

1. I assume some defective mRNA strands and lipid layers can be generated during the myriad of involved complex chemical processes. Do we understand percentage of defective nanoparticles / mRNA strands? Does process include QA that somehow reduces or eliminates potentially harmful defects. What is risk of defective mRNA strands that could encode for harmful proteins? Any other associated risks here that I am not addressing?

Given that the mRNA sequences in the Pfizer and Moderna vaccines are synthetically produced, I would say that there are very few defective mRNA sequences. And, when it comes to producing proteins based on these few defective sequences, the additional risk from such defective sequences for the human body would be, effectively, zero. In fact, a few slight variations in the protein sequence for the spike protein would only result in slight variations in the immune system response. And, producing such slight variations are already part of how our human immune system is programmed to work – automatically producing slight variations in the antibodies produced against a particular type of foreign antigen, for example.

2. How much independent review occurred with these vaccines? Is the Global Advisory Committee on Vaccine Safety the only body that reviewed. Do scientiests get hands-on and eyes-on access to the actual chemical processes to verify what is happening (in vitro and in vivo), or are they just provided with white papers and reports for review?

A great many scientists were involved in the production and review of the mRNA vaccines. These vaccines, how they work, and their effects on human biochemistry are very well known by a great many scientists who work in this field of immunochemistry. There are no fundamental secrets here.

3. Some papers and FAQs claim the generated viral “spike protein” is presented on the cell surface. Some of your dialogue here seems to indicate that this is not the case. Which is it? How is it presented? Is it presented in a variety of ways?

Here are a few diagrams that illustrate what’s happening within different cells of the body where the mRNA sequences are decoded and presented:

Mechanism of action of mRNA vaccines. 1. The mRNA is in vitro transcribed (IVT) from a DNA template in a cell-free system. 2. IVT mRNA is subsequently transfected into dendritic cells (DCs) via (3) endocytosis. 4. Entrapped mRNA undergoes endosomal escape and is released into the cytosol. 5. Using the translational machinery of host cells (ribosomes), the mRNA is translated into antigenic proteins. The translated antigenic protein undergoes post-translational modification and can act in the cell where it is generated. 6. Alternatively, the protein is secreted from the host cell. 7. Antigen protein is degraded by the proteasome in the cytoplasm. The generated antigenic peptide epitopes are transported into the endoplasmic reticulum and loaded onto major histocompatibility complex (MHC) class I molecules (MHC I). 8. The loaded MHC I-peptide epitope complexes are presented on the surface of cells, eventually leading to the induction of antigen-specific CD8 + T cell responses after T-cell receptor recognition and appropriate co-stimulation. 9. Exogenous proteins are taken up DCs. 10. They are degraded in endosomes and presented via the MHC II pathway. Moreover, to obtain cognate T-cell help in antigen-presenting cells, the protein should be routed through the MHC II pathway. 11. The generated antigenic peptide epitopes are subsequently loaded onto MHC II molecules. 12. The loaded MHC II-peptide epitope complexes are presented on the surface of cells, leading to the induction of the antigen-specific CD4 + T cell responses. Exogenous antigens can also be processed and loaded onto MHC class I molecules via a mechanism known as cross-presentation. (Link)

Now, The mRNA-1273-encoded prefusion stabilizes the S protein (Moderna Vaccine) consists of the SARS-CoV-2 glycoprotein with a transmembrane anchor and an intact S1–S2 cleavage site. The presence of the transmembrane anchor would seem to enable some of the spike proteins to remain attached to the surface of the cell that produced them, such as a muscle cell, but would still be recognized as “foreign” by the immune system. (Link)

See also: Link


Are mRNA Vaccines for COVID-19 helpful or harmful?
The following commentary by organic chemist Derek Lowe is also helpful in understanding this question (December 4, 2020):

Bob Wachter of UCSF had a very good thread on Twitter about vaccine rollouts the other day, and one of the good points he made was this one. We’re talking about treating very, very large populations, which means that you’re going to see the usual run of mortality and morbidity that you see across large samples. Specifically, if you take 10 million people and just wave your hand back and forth over their upper arms, in the next two months you would expect to see about 4,000 heart attacks. About 4,000 strokes. Over 9,000 new diagnoses of cancer. And about 14,000 of that ten million will die, out of usual all-causes mortality. No one would notice. That’s how many people die and get sick anyway.

But if you took those ten million people and gave them a new vaccine instead, there’s a real danger that those heart attacks, cancer diagnoses, and deaths will be attributed to the vaccine. I mean, if you reach a large enough population, you are literally going to have cases where someone gets the vaccine and drops dead the next day (just as they would have if they *didn’t* get the vaccine). It could prove difficult to convince that person’s friends and relatives of that lack of connection, though. Post hoc ergo propter hoc is one of the most powerful fallacies of human logic, and we’re not going to get rid of it any time soon. Especially when it comes to vaccines. The best we can do, I think, is to try to get the word out in advance. Let people know that such things are going to happen, because people get sick and die constantly in this world. The key will be whether they are getting sick or dying at a noticeably higher rate once they have been vaccinated.

No such safety signals have appeared for the first vaccines to roll out (Moderna and Pfizer/BioNTech). In fact, we should be seeing the exact opposite effects on mortality and morbidity as more and more people get vaccinated. The excess-death figures so far in the coronavirus pandemic have been appalling (well over 300,000 in the US), and I certainly think mass vaccination is the most powerful method we have to knock that back down to normal.

That’s going to be harder to do, though, if we get screaming headlines about people falling over due to heart attacks after getting their vaccine shots. Be braced.


Are mRNA Vaccines for COVID-19 helpful or harmful?
I know that various European countries, including the Netherlands, Denmark, and Spain, have reported outbreaks of COVID-19 in mink pelt farms – leading to the culling of more than a million animals. From laboratory experiments, it’s also clear that ferrets (a relative of the mink) are also readily infected with the “novel coronavirus”. Aside from this, however, I’m not aware of any “issues” with animal experiments regarding COVID-19 in particular. However, in 2008 there was an interesting experiment involving ferrets that were given the flu vaccine against the H1N1 virus – who then became sicker once exposed to the live virus as compared to those ferrets that weren’t vaccinated. The reason for the effect was unclear, and Skowronski, the lead author, urged other research groups to take up the question.

“Skowronski likened the mechanism to what happens with dengue viruses. People who have been infected with one subtype of dengue don’t develop immunity to the other three. In fact, they are more at risk of developing a life-threatening form of dengue if they are infected with one of the other strains.”

Skowronski called the second theory the infection block hypothesis. Having a bout of the flu gives the infected person antibodies that may be able, for a time, to fend off other strains; flu shots only protect against the strains they contain. So under this theory, people who didn’t have flu in 2008 because they got a flu shot may have been less well armed against the pandemic virus.”

While interesting, such an effect has not been identified in the animal or human trials for the mRNA vaccines against COVID-19. Also, subsequently updated flu vaccines to the H1N1 strain haven’t had this problem either (Link).