Southern Adventist University opens Origins Exhibit
@pauluc:

If I may summarize our previous posts on allelic variation, SNPs and speciation
You suggest

1] There was frontloading of genetic information in a breeding pair for most species 2349-2348 BC.

The frontloading was at the time of creation by the Creator (less than 10,000 years ago), with a genetic bottleneck at the time of the Noachian Flood some 4,000 or so years ago . . .

2] Variation leading to speciation within kinds was by genetic mechanisms of allelic variation from the original gene pool. Maybe 10-20% of the variation can be attributed to this front loading.

It depends what type of variation you’re talking about. All of the variation beyond very low levels of functional complexity is the result of frontloading . . .

3] Most of the allelic variation and SNPs seen in species today has arisen by random mutation within the populations derived from this starting population of 4 haplotypes. ie 80-90% of the variation within species derived from “kind” ancestor.

At low levels of functional complexity, yes, the vast majority of allelic variations are the result of random mutations.

4] Most (80-90%) of the phenotypic differences seen between species has occurred by natural selection and genetic drift.

Within the same basic “kind” of gene pool – yes.

5] Any differences due to RM/NS after selecting the front-loaded pair can only confer very very low level complexity.

That’s right.

6] There is a barrier of 1000fsaar that limits any ability to generate anything novel and complex within this 80-90% of new mutations.

Yes.

Apropos of the recent paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310774/?tool=pubmed

How do you modify your model of constraint by 1000fsaar to account for the role of SNPs in determining the effects of non-coding regulatory elements? In this context any discussion of hamming distance is really examining the edge effect of minimal relevance. I should not have to explain how this is particularly germane and impacts your discussion about genetics of feathers and the regulation of genes controlling feathered phenotype.

Non-coding regulatory elements are key to the building of complex systems within living things – far more important than are the protein-coding genes themselves (which function more like bricks and mortar that can be used to create many different types of buildings). SNPs can affect these regulatory elements, obviously. However, SNPs cannot affect these regulatory elements in a way that causes them to produce a qualitatively novel type of “building” with the “bricks and mortar” – beyond very low levels of functional complexity of course. In other words, you have to ask yourself the odds that a single point mutation to a regulatory non-coding sequence, or any other type of mutation, will result in a change in the location of the final product to an entirely novel island in sequence space that has a qualitatively unique function that requires a minimum of more than 1000 specifically arranged amino acid parts? That just doesn’t happen. There are no examples of this anywhere in literature – period.

If you would actually sit down and do the math, you’d see why. Sequence space has a fairly uniform distribution of potentially viable sequences/structures. As the minimum size and or specificity of the system under consideration increases in a linear manner, what do you think happens to the ratio of potentially viable/beneficial vs. non-viable/non-beneficial sequences in sequence space? The number of non-viable sequences increases in an exponential manner compared to the potentially viable sequences. The means that the viable sequences become more and more isolated in sequences space, dramatically so, with each step up the ladder of minimum size and/or specificity requirements. This means, of course that the minimum likely gap distance between viable sequences in different island clusters increases in a linear manner with each increase in the minimum size and/or specificity requirements. And, this means, of course, that the average time needed for any kind of random mutations needed to traverse the linearly increasing gap distances increases exponentially.

Now, tell me, how do you solve this sequences/structure space problem at increasing levels of functional complexity? Do you really not see the exponential nature of the problem? There is really no point in further discussion if you will not discuss this particular question. I really don’t understand your continued reluctance to substantive address such problems or consider the statistical basis for your own evolutionary assumptions. Why don’t you sit down and actually do a few calculations? Why not calculate the odds, for yourself, of any kind of mutation or series of mutations in any kind of coding or non-coding region evolving any kind of qualitatively novel system at various levels of functional complexity?

Give it a shot already. What could it hurt?

Sean Pitman
www.DetectingDesign.com

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Southern Adventist University opens Origins Exhibit
@pauluc:

Since you havent responded to my request to identify in the genomic comparison of mammalian species or primates with the instances of where the 1000fsaar criteria limiting the sequence differences, I suggest an alternative.

But I have responded to this question at least a couple times in this thread. Please go back and review these responses to you and Jeff Kent.

Please provide insights on this recent paper from Kate Sullivans group on Human Accelerated Regions that are proposed to be contributors to the differences between humans and Chimps particularly in limb and brain development. Im interested in the comparison between human SNPs and the varying presence of these SNPs in chimp, Neandertal and Denisova genomic sequences.

Differences between human and ape brain development are based on more than SNPs (which would produce quantitative differences in form and function, but not produce qualitative changes beyond very low levels of functional complexity).

As already noted a few posts above in this thread, humans and apes are quite different in various respects, to include brain structure and function – which is thought to be based on numerous differences in genetic regions that code for miRNAs (around 8% of which are human specific).

“miRNAs recently have been implicated in synaptic development and in memory formation. As the species specific miRNAs described here are expressed in the brain, which is the most complex tissue in the human body, with an estimated 10,000 different cell types, these miRNAs could have a role in establishing or maintaining cellular diversity and could thereby contribute to the differences in human and chimpanzee brain … function.”

Eugene Berezikov, Fritz Thuemmler, Linda W van Laake, Ivanela Kondova, Ronald Bontrop4, Edwin Cuppen & Ronald H A Plasterk, “Diversity of microRNAs in human and chimpanzee brain”, Nature Genetics, Vol 38 | Number 12 | December 2006 pp. 1375-1377.

The Y-chromosome is even more unique. A study published by Nature in early 2010 showed many striking differences between human and chimp chromosome structure, gene content, and even qualitatively unique genes between the two species.

As far as looking at specific genes, the chimp and human Y-chromosomes seem to have a dramatic difference in gene content of up to 53 percent. In other words, the chimp is lacking approximately half of the genes found on a human Y-chromosome. Because genes occur in families or similarity categories, the researchers also sought to determine if there was any difference in actual gene categories. They found a shocking 33 percent difference. The human Y-chromosome contains a third more gene categories, entirely different classes of genes, compared to chimps.

Hughes, J.F. et al. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure gene content. Nature. 463 (7280): 536-539.

For further discussion see:

http://www.detectingdesign.com/pseudogenes.html#Key

I am sure you see P Troglodyes as entirely unrelated to man but I am a little unclear on your model of origins in terms of relatedness of Neandertal and Denisova hominids to man. Are they the children of Adam, Noah or neither? How do you account for any sharing of SNPs, the HAR and the development of pehnotypic differences by SNPs?

Neandertals and Denisova are human, descendants of Noah. They are simply ethnic variations of humans. Even mainstream scientists think that they could interbreed with each other to produce viable and virile offspring.

Of course there will be SNP differences between modern humans and Neandertals and other ancient ethnic groups – as there are between modern ethnic groups. And, these SNPs may be associated with functional differences – but not beyond low levels of functional complexity (usually only quantitative differences of the same basic type of gene function).

As far as the HAR-1 RNA, there are 18 character differences between humans and chimps (out of 118 characters/nucleotides). These differences are thought to play some role in the development of our brain differences, but no one knows exactly what role. Obviously, there are many structural and functional brain differences at high levels of functional complexity. However, there are also many unique non-coding genetic elements that seem to be involved with these differences (as already explained). No single point mutation or small cluster of mutations is going to be able to cross the gap between any qualitatively novel higher level system of function. Again, there are no examples of this in literature – for very good statistical reasons.

Another paper that cries out for your interpretation including the point at which ignorance about the 1000fsaar limit has blinded this group of scientist.

http://www.ncbi.nlm.nih.gov/pubmed/22398555

Critique below the abstract would be most helpful in seeing the errors.

Where in this paper is there any discussion of levels of functional complexity and how mutations can generate qualitatively novel systems at high levels of functional complexity? Remember, we aren’t just talking about quantitative differences in functionality here. We are talking about qualitatively novel differences beyond low levels of functional complexity. We need some actual math here – a few statistical calculations as to the odds that the just-so stories in papers like this might or might not actually be likely to be realized in a given span of time. Please do quote for me the relevant portion of this or any other paper along these lines.

Don’t just give me a bunch of references without any quotes or commentary (aka: reference mining). Show me that you actually understand the problem under discussion by, well, discussing it for a change with the use of quotes that you think are relevant. That would be most helpful…

Sean Pitman
www.DetectingDesign.com

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Southern Adventist University opens Origins Exhibit
@Professor Kent:

Again, the question is why does one accept the Bible among so many compete options as the real Word of God? If this choice is based on blind faith without any rational basis or appeal to the weight of empirical evidence, what you have is nothing much more useful than wishful thinking… not the kind of faith that has the power to provide a solid hope in the future for most rational people – especially in the face of very difficult trials or even the threat of torture and death.

What you’re asking people to do is to accept the Bible without really considering the weight of empirical evidence or any additional evidence that may contribute to the current weight of evidence for or against the Bible’s credibility. That’s simply not a rational expectation. Certain God does not expect anyone to believe without a rational basis for belief or faith set upon the weight of evidence that would appeal to the candid mind.

In this line, we are talking about what paid representatives of the SDA Church are teaching and/or preaching in the name of the Church. The Adventist Church, as an organization, simply cannot afford to pay people to go around teaching our young people that the best we have to support the Adventist position on origins is faith that is effectively blind to the otherwise overwhelming scientific basis for neo-Darwinism. That simply isn’t helpful to Adventism. Those who believe in neo-Darwinism, however honest and sincere they may be (and there are many in this category) cannot effectively represent the Adventist perspective on several fundamental doctrinal positions within our schools…

Sean Pitman
www.DetectingDesign.com

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Liberty & Health Alliance – An Appeal for Action
While recommending the vaccines, the vaccine statements clearly left the decision to vaccinate, or not, to the individual. They had nothing to do with government funding (yet another conspiracy theory). These statements were issued in an honest effort to save lives, not to make money. The “medical minds” at the BoT Symposium generally support anti-vaxxers and conspiracy theorists like Peter McCullough who are known for promoting misleading or downright false claims regarding the pandemic and the mRNA vaccines.

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Liberty & Health Alliance – An Appeal for Action
Pastor E.L. has also written (FB Post) an excellent explanation in defense of the affirmation statement and our denomination’s position on vaccines.

“The assumedly troublesome wording commonly highlighted concerning this issue is a misreading of intent in context, without trying to understand the sense in which it can be understood as harmonious with the rest of the statement which strongly affirms individual conscience. A charitable reading first attempts to understand what someone says in a sense that is harmonious, rather than immediately assuming they intend to contradict themselves.

The trajectory of the context in the Reaffirmation Statement suggests that when it asserts, “Claims of religious liberty are not used appropriately in objecting to government mandates or employer programs designed to protect the health and safety of their communities,” this is likely because the church has not established a doctrinal position on vaccines that would require uniform adherence among its members. If it had, such a stance would then necessitate the church to defend it as a matter of religious liberty.

The issue of vaccination is multifaceted, and adopting a definitive for or against position within church doctrine would infringe on the rights of those who hold opposing views. Instead, the document consistently emphasizes that this is a matter of individual conscience and underscores the church’s support for such personal discernment. Accordingly, it states: “We recognize that at times our members will have personal concerns and even conscientious convictions that go beyond the teachings and positions of the Church. In these cases, the Church’s religious liberty leaders will do what they can to provide support and counsel on a personal basis, not as a Church position, even at times assisting members in writing their own personal accommodation requests to employers and others.”

In essence, while the church has not elevated this issue to a doctrinal level requiring institutional defense, it remains committed to supporting individual religious convictions to the greatest extent possible. Personal convictions are respected and defended, even though the church as a whole has not taken—and could not reasonably be expected to take—a uniform doctrinal position on the matter.

To draw an analogy, Seventh-day Adventists could not argue that wearing head coverings in the workplace is a religious liberty issue because it is not a doctrinal requirement within the SDA faith, even though it is mentioned in the Bible. Instead, they could only frame it as a matter of personal conviction if they interpret the biblical instruction as still applicable today. While individual SDAs who support head coverings may personally view it as a religious liberty concern, the distinction lies in the fact that religious liberty claims are typically based on doctrines that a religion universally requires of all its adherents.

In contrast, Muslims can assert that head coverings are a doctrinal religious liberty matter because it is a doctrinally mandated practice within Islam. This highlights the difference between personal convictions and doctrines that are formally upheld by a religious institution when speaking of “religious liberty.”

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Liberty & Health Alliance – An Appeal for Action
Pastor Wyatt Allen (one of the founders of the Liberty & Health Alliance) wrote in a FB Comment:

Two things your article lacks are compassion and understanding. The first would lead to the second. Should I have more time tomorrow, I’ll try to be more specific and why I make this claim. Though anybody reading it would see the lack of compassion. I think the lack of understanding essentially boils down to misrepresenting what we’re saying. COVID and the mandates might be passed. But unless we learn from our mistakes during this time (do you say the church made no mistakes?) we will be unprepared to help in the next crisis. And when we are unprepared to help in a meaningful way, it really does hurt people. Actual people. As a minister of the gospel, I have seen the tears, I have heard the pleas, I have witnessed the freedom being ripped away. We can theorize and write articles all day long about Liberty. But until we actually stand up for it, all that comes across is coldness.

My response:

You seem to suggest that I’m opposed to religious liberty and that I don’t care for those who suffered. How can you know this? I mean, I am a strong supporter of religious liberty and have experienced personal serious attacks on my own religious convictions. While in the army I was brought up for court martial twice for refusing orders to work on Sabbath in ways that I thought were opposed to God’s commands regarding the Sabbath. I was threatened with jail time, the loss of my career, and financial damages. So, you see, I’m very much aware of how it feels to be personally threated for my own religious convictions. I also understand why someone who is opposed to vaccines would blame the Church for a lack of support during the vaccine mandates.

It’s not that I don’t understand. It’s that I think that such efforts to blame the Church and the Vaccine Statements are misdirected since these Vaccine Statements repeatedly and specifically support individual choice in this matter. Recommendations regarding medical interventions, like vaccines, do not undermine personal religious liberties or the Church’s support for such liberties. The claims of the Liberty & Health Alliance to the contrary simply do not make sense to me. Even if the Church had no vaccine statements at all, I fail to see how this would have helped anyone during the vaccine mandates.

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Additional responses to other comments from Wyatt on FB:

Wyatt Allen: You’re also asking Charles Downing (not sure of his medical background) to explain to me that the “so-called vaccines” have too many adverse reactions. You see, right there you’re showing your hand. The reason why you’re so passionate against the Vaccine Statements of the Church is because you truly believe them to be harmful and evil. While I sympathize with why you feel this way, consider that I feel the very same way for the opposite reasons. I saw ICUs filled with the very sick and the dying during the pandemic, the significant majority of whom were the unvaccinated. Several of my own workers who refused to get vaccinated ended up in the ICU and two suffered permanent injuries so severe that they can no longer work full time. Many more from my own church and community ended up in the ICU for the same reason. More than a dozen of my own family friends died because they didn’t get vaccinated. My brother-in-law, the well-known pulmonologist Dr. Roger Seheult saw many many more die while holding their hands in his ICU in S. Cal – even some who were young and vegan and otherwise healthy. So, yes, we are both very passionate about this topic. It’s one of the reasons why I try to force myself to be as objective as possible when I talk about this topic.

The reason why I disagree with you and Charles here is because I think you have a misunderstanding of the risk/benefit ratio for the mRNA vaccines and vaccines in general. You don’t understand the nature of VAERS (which is maintained by the NIH and the CDC by the way) since you don’t seem to understand the difference between correlation and causation. The VAERS database is used to sort out this difference. The claim of Charles that the spike protein produced in response to the mRNA vaccines sends the human immune system into “overdrive” and “taxes” and “weakens” it is false. This isn’t how the human immune system works. The spike proteins are broken down into small pieces called “antigens”, which are then presented to T- and B-cells so as to educate them to know what to attack in the future. This process happens every day and does not tax or weaken the immune system in the least. I mean, consider that a C19 infection would produce far far more spike proteins throughout the entire body for a much longer period of time. The mRNA vaccines, in comparison, are self-limited and are largely localized. Charles’ claim that the vaccines have produced a 40% spike in cancer rates and “turbo cancers” is also a false claim based on the claims of conspiracy theorists. I’m an anatomic and clinical pathologist with a subspecialty in blood disorders. I diagnose cancers every day. That’s what I do. I can tell you that there has been no increase in cancers associated with the mRNA vaccines. Beyond this, there is no mechanism by which the mRNA vaccines could produce such a spike in cancer rates. As far as Charles’ claim that the vaccines were not “thoroughly studied”, this is also a false statement. The mRNA vaccines went through all of the standard steps for vaccine testing and approval – to include double-blinded placebo-controlled animal and human trials with great success. There were no increased deaths, much less “25 deaths”, and the “adverse reactions” were minor and not beyond the expected rate in the 70,000 human volunteers. Also, the mRNA technology itself is not new, but has been studied now for over 30 years. It’s just that all of the necessary technological information came together at just the right time for the mRNA vaccines to make it to the general public soon after the pandemic hit. That’s just the nature and usefulness of the mRNA technology which Charles doesn’t seem to understand.

Conrad Vine Continues to Attack Church Leadership

Dr. Peter McCullough’s COVID-19 and Anti-Vaccine Theories

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Wyatt Allen: I’m not sure what important question(s) of yours I failed to answer? Please do point these out to me again so that I won’t inadvertently skip over something that is important to you.

Regarding your current question, of course I make mistakes all the time. In my job as a pathologist I try to be extremely careful to limit my mistakes, but mistakes do happen since we are all human and subject to error. I often wish I had a “redo” button available to me so that I could go back in time and fix some of my mistakes.

I know that you believe that your argument (regarding all vaccines I think) is based on the Bible and the Spirit of Prophecy – and I respect that even though I don’t agree with you here. However, you are promoting your anti-vaccine position since you have presented numerous arguments against vaccines. I think these arguments are based on mistaken concepts and ideas, but, again, this is the reason for personal and religious liberty as long as these liberties don’t interfere with those of another.

I also understand that you want to plead for those who cannot effectively plead for themselves. I’m trying to do the same thing. I think that the misinformation presented by you and many others (particularly those like Dr. Peter McCulough) have caused untold injuries and deaths to many who would have been saved by being vaccinated. I also have no doubt there were those who misused the Vaccine Statements of the Church regarding mandates. While this shouldn’t have happened, again, I fail to understand how this is the fault of the Church? The Church has published many statements that have been misused. The same is true of many of the statements and claims found in the Bible itself. Is this the fault of the Bible? Should the Bible be rewritten because some of its language is confusing and difficult to properly understand by the many who have misinterpreted and misused it?

You keep repeating that the Vaccine Statements “exalt peer-reviewed scientific literature to the level of the Bible” – and that if I don’t see it this way that I should read them again. I’ve read them dozens of times and I still don’t see how you could possibly make this amazing, even shocking, claim. None of the leaders of the SDA Church would ever think to suggest such an idea – verbally or in writing. Certainly, no Christian physician or scientist would promote such a concept either. So, where are you getting this idea? The Vaccine Statements themselves make no such claim – not even close.

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Wyatt Allen: The claim that the Vaccine Statements elevate peer-review literature equal to the Bible simply isn’t true. This claim is particularly shocking to me. I’m not sure how anyone could interpret these statements in this way? These statements are not statements of Fundamental Beliefs or doctrinal statements at all. They are simply general *recommendations*, not decrees or anything like that, regarding advances in medical science. That’s it. They specifically note that they are not to be considered doctrinal or in any way binding regarding the conscience of the individual – that the final decision is and should be with the individual regarding such issues.
Yes, words do matter, but in this case, I fail to see how your claims regarding the Church’s Vaccine Statements are valid or helpful moving forward since I fail to see how these Statements undermine individual religious liberty.

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Weston Greenwood: One can do both you know. I also advocate for both. I strongly believe the mRNA vaccines were a miraculous gift from God that saved millions of lives and prevented many many more hospitalizations and long-term injuries. At the same time, I’m also a strong supporter of personal and religious liberty – particularly for those who disagree with me. In the same way, the Vaccine Statements promote the benefits of vaccination while, at the same time, noting that one is perfectly free to disagree – and that this decision should take precedence.

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Weston Greenwood: The Church did bring this to a vote via the delegates at the last GC Session. It’s just that this vote went against you.

Liberty & Health Alliance – An Appeal for Action

Again, if an employer bases his/her decision to mandate vaccination on the Church’s Vaccine Statements, then that employer is misusing these statements – which isn’t the fault of the Church.

And yes, just because the Church does not stand in the way of someone who wants to get vaccinated, and even encourages this, doesn’t mean that it, therefore, stands in the way of someone who doesn’t want to get vaccinated. Claiming otherwise makes no sense to me.

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Wyatt Allen: You’re essentially saying that, “Any outsider who reads the ADCOM statement will see it as binding”.

If someone does read it that way, they aren’t reading it correctly because that’s not what it says. It says that while the SDA Church, as an organization, is not inherently opposed to vaccines and recognizes their usefulness, it remains with the individual and individual conscience as to the final decision to get or not to get vaccinated – that it is not an issue of morality, is not a matter of salvation, and is therefore not doctrinal. That’s what it says. Those who read it otherwise for the purposes of enforcing mandates based on such Statements are clearly misusing them. And, obviously, such misuses are not the fault of the Church.

Also, contrary to your claim, the Church has not elevated peer-reviewed literature published in scientific journals to the level of Scripture. That’s a completely false and completely unfair claim – particularly directed at medical professionals like me who recognize the usefulness of vaccines while, at the same time, recognizing the final authority of the Bible in all questions of faith. It’s just that I don’t see where the Bible speaks against vaccines anywhere in its pages. The same is true for the Spirit of Prophecy.

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Conrad Vine Continues to Attack Church Leadership
I think that there can be a reasonable combination of the best of modern medicine as well as the best of healthful living and natural remedies such as exercise, sunlight, vitamin D, “forest bathing”, good sleep, vegan or at least a vegetarian diet, etc…

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Conrad Vine Continues to Attack Church Leadership
You opted not to get vaccinated during the pandemic, for whatever reason, but did not advise others to do the same. That’s fine. I think you probably increased your own risk a bit, but that’s far better than giving medical advice to others when you don’t know for sure that you’re right – especially for those who were at higher risk than you. It’s also good that you supported others who did choose to get vaccinated.

As far as SDA hospitals and organizations, I agree that there has been some drift from the ideal. I’m not happy that so many non-SDAs are hired to work in and to be leaders. I’m also disappointed that there isn’t a lot more emphasis, direction, and teaching with regard to healthful living. There are some who are doing this, like Dr. Roger Seheult. However, there does seem to be a lack of an organized or official emphasis on how to living healthful so as to avoid having to use so many medications for chronic conditions that are largely self-inflicted. Now, I do sympathize that quick fixed and pills are what most patients want. Most doesn’t want to give up their back health habits, so doctors often just give up and give their patients what they want. Still, this does not excuse the lack of effort along these lines in our hospitals and medical schools. Also, more should be done to spread the Gospel Message in our hospitals as well…

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