Bill Basener (a participant here) co-authored a paper with John Sanford. He was given the honor of delivering a KEYNOTE ADDRESS at an international SECULAR biology conference. A video of his presentation is available in a link inside my write up of his presentation below. He alluded to some of the helpful input from his critics at TheSkepticalZone in his talk:
http://crev.info/2018/07/keynote-speech-falsifies-darwinism/
John Sanford is sort of the “Papa John” of creationist genetics. It is customary for the leader of a research group to be listed as the last author in a publication. That convention is seen in a variety of papers and books such as Rupe & Sanford; Basener & Sanford; Carter, Lee & Sanford; Montanyez, Fernandez, Marks & Sanford; and let’s not forget the Legendary High Velocity Team of Klein, Wolf, Wu & Sanford that permanently ensured the infusion of intelligently designed genes into a sizable fraction of Genetically Modified Organisms on planet Earth.
And perhaps one day in the distant future there will be a paper, “Cordova & Sanford”! 🙂
Below is a link of a paper from Papa John’s team about Adam and Eve which will be presented this week, July 29,2018 – August 1, 2018 at the 8th International Conference on Creationism
http://www.creationicc.org/2018_papers/15%20carter%20Y%20chromosome%20final.pdf
The existence of a literal Adam and Eve is hotly debated, even within the Christian body. Now that many full-length human Y (chrY) and mitochondrial (chrM) chromosome sequences have been sequenced and made publicly available, it may be possible to bring clarity to this question. We have used these data to comprehensively analyze the historical changes in these two chromosomes, starting with the sequences of people alive today, and working backwards to the ancestral sequence of the family groups to which they belong. The analyses of the chrY and chrM histories were done separately and in parallel. Remarkably, both analyses gave very similar results. First, the pattern displayed in both datasets supports a massive expansion of the human lineage, with multiple new branches forming from closely related individuals. Second, for both chromosomes, the mutation rate along each branch has not been the same through time. Third, both phylogenetic trees display a starburst pattern that centers around specific historical individuals, nearly all of whom lived in the Middle East. Fourth, we can know with a very high degree of confidence the actual sequences of the historical individuals that gave rise to each branch in both family trees. Fifth, within a reasonable margin of error we can approximate the sequence of Y chromosome Adam/Noah and Mitochondrial Eve. Sixth, given a few reasonable assumptions, we can estimate the time to Y Chromosome Adam/Noah and Mitochondrial Eve. Both individuals lived less than 10,000 years ago, which is most consistent with a biblical timeframe. Lastly, recurrent mutations are extremely common, and many of them are associated with epigenetic CpG sites, meaning mutation accumulation is not free of environmental influence and many mutations may have accumulated in different lineages in parallel. The genetic evidence strongly suggests that Y Chromosome Adam/Noah and Mitochondrial Eve were not just real people, they were the progenitors of us all. In this light, there is every reason to believe that they were the Adam/Noah and Eve of the Bible.
NOTE: Paul Nelson’s family was instrumental in the founding of the International Conference on Creationism which meets every 5 years. Paul is one of the few ID proponents openly associated with YEC. Nelson gave the 2013 ICC Keynote Address on Orphan Genes.
Funny, looks to me that it’s the exact opposite that transpired in that thread.
As is so often the case, what you say is so full of unstated assumptions and allusions to your private thoughts that I don’t have a clear idea of what you’re trying to say here. Trees are generally rooted by outgroups. Of course in order to do this you have to agree that outgroups have some phylogenetic relation to the ingroup. If that’s what you call a “predetermined narrative”, then yes. But that narrative is based on very good evidence. Then again, if you can’t root a tree, or even constrain its root at all, then you’re saying the root could be anywhere on any branch, and in that case you can’t actually make any statement about migrations, population structure, or even sub-branches.
Sorry, what stuff about evolutionary rates? Why is it bogus? Try to remember that, unlike you, I don’t already know what you’re saying.
Can it? How?
When did I make any claims about molecular clocks? Who are you even arguing with here?
This is an interesting claim which I would like to see you develop with some actual evidence and argument. This is, to my knowledge, the first time you have claimed that each species is separately created. Or would you like to retract that claim in favor of some weaker claim?
I don’t think you know anything about how trees are rooted or what unrooted trees can communicate.
You still don’t understand what “unrooted” means and how little you can determine from an unrooted tree. Also, I have no idea what I am supposed to have objected to. I don’t even know what the trees you show are trees of, or what you think you’re getting from them.
Which other objections? Why are they substantive? Please explain what you think we’re talking about.
That’s a common fallacy. You people need to learn something about phylogenetics and population genetics before you can claim to overturn previous work. Nothing in that unrooted tree supports a bottleneck. Nothing in a rooted tree supports a bottleneck either.
Whereas suggesting that Adam & Eve had preformed gametes clearly is not “driven by pushing a pre-determined narrative”. LOL! Preformed ova and sperm, seriously? Why don’t you guys just bring back the homunculus, while you are at it?
Hmm on the topic of pushing pre-determined narratives here are some quotes:
“We’ve already said that it’s the Holy Spirit who gives us the ultimate assurance of Christianity’s truth. Therefore, the only role left for argument and evidence to play is a subsidiary role. I think Martin Luther correctly distinguished between what he called the magisterial and ministerial uses of reason. The magisterial use of reason occurs when reason stands over and above the gospel like a magistrate and judges it on the basis of argument and evidence. The ministerial use of reason occurs when reason submits to and serves the gospel… Should a conflict arise between the witness of the Holy Spirit to the fundamental truth of the Christian faith and beliefs based on argument and evidence, then it is the former which must take precedence over the latter, not vice versa.”
“The Bible says all men are without excuse. Even those who are given no good reason to believe and many persuasive reasons to disbelieve have no excuse, because the ultimate reason they do not believe is that they have deliberately rejected God’s Holy Spirit.”
– William Lane Craig, Reasonable Faith p. 36.
Craig is of course not unusual in this respect as similar things are affirmed by many christian and creationist organizations and institutions.
Anyone remember the Wedge Strategy Document, and not to mention Phillip Johnson’s motivations for the Intelligent Design movement?
“This [the intelligent design movement] isn’t really, and never has been, a debate about science, it’s about religion and philosophy.” – Phillip Johnson: World Magazine, 30 November 1996
“The Intelligent Design movement starts with the recognition that ‘In the beginning was the Word,’ and ‘In the beginning God created.’ Establishing that point isn’t enough, but it is absolutely essential to the rest of the gospel message.” – Phillip Johnson: Foreword to Creation, Evolution, & Modern Science (2000)
no, I just don’t see why it’s relevant to that topic that humans share alleles with chimps or chinchillas.
peace
We all have “pre-determined narratives” that we start with.
If you did not have a “pre-determined narrative” you would just have unconnected data.
What’s important is that your “pre-determined narrative” makes sense under it’s own terms before you try and attach the data to it.
peace
Right, so let’s compare “rooting a phylogenetic tree” with “front-loading Adam & Eve’s gametes with all the genetic variation we come to see in the present human population”. Haha, aren’t we both silly with our predetermined narratives? No, “we” are not, because these two things are not remotely comparable.
Rooting a phylogenetic tree with an outgroup makes perfect sense, since there is no reason to doubt that the taxon that one happens to be interested in is nested within a more inclusive group. That approach is supported by the massive amount of evidence we have for common descent and which is often discussed here at TSZ; the nested distribution of derived molecular and/or morphological characters, consilience of multiple independent characters and of course the fossil evidence. OTOH, smuggling in genetic variation into the reproductive apparatus of Adam and Eve by a completely unsupported conjecture because you need to force-fit a biblical story to the present amount of human genetic variation is [a-ha] a fig leave to hide a glaring discrepancy.
Sal,
In this context entropy would have to mean disorder…otherwise your comment/claim would make no sense…to me at least…
That’s a good objection, and that’s why I suggested the test of a bottleneck under evolutionary assumptions. So, I actually agree with you! We can model the bottleneck under evolutionary assumptions, and that’s why I propsed the model of comparing autosomal chromosome diversity with mtDNA, and it just occured to me it should work with Y-chromosomes.
So yes, ironically you’ve called my hand out on this one, and yes, I’m openly putting my reservations about one of Carter’s solutions. Ok, so you can criticize the model on those grounds, and you have no IMMEDIATE objection from me as far as this conversation SO FAR. Ok we can agree on your objection for the sake of argument.
Is it then your assumption that humans were separately created from all other species and have no genealogical relationships to them? If so, what would be the basis of that assumption? Many others would go with the evidence that your assumption is false, and would use phylogeny to test claims of a bottleneck.
And in fact chimps tend not to share alleles with humans in genes for which there is no expectation of frequency-dependent selection, so your rationale for shared alleles doesn’t fit the facts. If your idea were true, shared alleles would be nearly universal in the genome rather than being concentrated in a few sorts of loci.
Regarding the unrooted tree, Carter echoes some of my sentiments:
I presume A0 is the center of the starburst pattern, some hypothetical “outgroup”.
Carter said earlier:
The midpoint (the arrow) on the unrooted trees looks to me to be the standard evolutionary starting point.
Why would you make that claim? I see no reason for it. You are once again assuming that the neighbor-joining tree is rooted when it is not. No outgroup is displayed or implied by the graphic. You have to pick your own outgroup or root after the analysis, if you want there to be one.
What “looks to me” is seldom the case when you bring these things up. You can choose to root a tree at the midpoint, which assumes a molecular clock. Such an assumption may be problematic, so this is seldom done. You can root with a known outgroup, which for humans ought to be a chimpanzee, or for most sequences a neandertal or denisovan. But of course you deny, a priori, that at least the first is related to us. I don’t think there’s any way for you, specifically, to root a tree given your assumptions, other than by misunderstanding what you’re doing.
Have you considered reading Joe’s book before trying to do phylogenetics?
Yes, this is a good way to try to understand some of Joe’s principles since, out of necessity, some of the ideas were abstract and tersely stated.
Thanks for what you just said, that was very informative and instructive.
Don’t you see that’s problematic and circular reasoning? 🙂 That’s exactly something that never bothers you except when creationists use it (which bothers me, both when creationists and evolutionists use it). So yes, what you just said is exactly why I don’t have high regard for some phylogenetic methods except to the extent it shows how much evolutionary theory is built on circular reasoning. The way out of the circular reasoning is to demonstrate “proofs by contradiction” which I think is feasible in the matter of the 2-person bottleneck model (even under evolutionary assumptions).
But that said, what do you make of the parallel starburst patterns in Ychr and Mchr? Looks to me there is A0 is a legitimate ancestor to the rest of the starburst except that really long tail going out to the right at A1. Agree? In fact A0 and L0 look like a legitimate bottle neck. Yes? No? Carter pointed out in the talk the pattern of a polytomy or whatever that means, something that is not a bifurcating branching tree.
No. It’s supported by a great mass of data. It relies on two assumptions: that humans are monophyletic, i.e. all related more closely to each other than to chimps, and that chimps are in fact related to humans. I call those assumptions but the evidence that they are both true is overwhelming. The point is that the reasoning for neither is circular.
No, it shows how little you understand of phylogenetics and evolutionary theory, nothing more.
I have no idea what you just said there. What do you mean?
No. If you actually look, the long tail is A0. And those patterns are parallel only graphically, in that the longest branch in each has been stretched out to the right, leaving a cluster of shorter branches on the left.
No. You don’t know what a bottleneck looks like, and the pattern isn’t a polytomy. Neither of you seems capable of reading the tree.
No it’s not. Similarity of some genes does not imply orphan genes and other orphan systems can evolve, in fact they would have to evolve outside of ordinary mechanisms such as those mechanism which drive gene based phylogenetic methods (which obey nayman pearson statistics, to quote someone from Joe’s Book). So, as usual, evolutionists unwittingly rely on statistical miracles (such as the origin of orphans) to make their theory work.
But anyway, I notice a very bad mistake on my part. A0 is on the extreme right of the Ychr graph, not the center. I was wrong about that. My mistake.
OK, I think this is the CENTRAL organizing theme of Carter, Lee, Sanford’s paper:
Hence we should not have some of the polytomies.
This is the graph showing the variability of mutation rates through long term evolution, hence Carter et. al argue the invalidity of the molecular clock hypothesis, and propose the long branch from starburst pattern could be due in part to a breakdown in DNA repair in addition to other factors. This is a testable prediction, as sadly, it predicts that branch will be more vulnerable to diseases associated with DNA repair. Anyway here is the graph:
Yikes, let me try again.
Click this link to enlarge:
http://theskepticalzone.com/wp/wp-content/uploads/2018/08/lenski_graph.png
Not one of those assertions is true, and you have certainly shown that you don’t know enough to evaluate any of them, even if you can quote random phrases from Joe’s book.
Is it possible that you noticed it because I told you about it?
As has already been observed, neither you nor you friends seem able to recognize polytomies or their absence, much less explain them.
What does the molecular clock hypothesis have to do with human evolution? What do mutator alleles in E. coli have to do with human evolution? What is the point of claiming that some human populations have mutator alleles (presumably for mitochondrial replication only?)?
I’ve said this before: you need to make some kind of coherent argument rather than vaguely alluding to mysteriously connected bits. And you never explain what you think you’re talking about despite numerous requests. One might speculate that it’s because you are uninterested in communication.
Maybe I shouldn’t have used the term, rather I should have said, “molecular clock” and omitted the term “hypothesis”. So the point is, the molecular clock could not be used, necessarily to dismiss the interpretation that the long branch came from the starburst center.
It’s possible, but I was looking Carter’s paper before I got to that part of your comment since I was responding to one part of your comment.
I am writing incoherently because I don’t understand, that’s why I’m communicating with you to help set me straight.
Sal, you’re still a creationist? Is there no evidence that will change your mind?
I’m a creationist too.
Nope. 🙂
Then you should realize that you don’t understand and not try to have any claims at all. You are presenting claims, all of which you should drop. So, apparently, should your friends, since if you are communicating their ideas correctly they don’t understand either. Incidentally, there is no “starburst”; that too, like the supposed similarity of the two unrooted trees, is just an artifact of the graphical display of the unrooted tree. No starburst, no bottleneck, no increased mutation rate, no time-direction. All of that is your imagination.
Hi Rich. Yes I’m still a creationist, moreso than before. That said, there are some tools in evolutionary biology that are useful in evaluating the Y-chromosome and the “M” chromosome.
What would change my mind? A viable solution to the origin of life problem.
That said, John Harshman, has corrected a lot of things in my misunderstandings. Not many people on the net will I admit mistakes to so quickly as in my interactions with John Harshman or Joe Felsenstein or Tom English and definitely the physicists like Olegt and Mike Elzinga. I most certainly don’t give ground to the others like Keiths or DNA Jock because their arguments are usually sub par.
Isn’t that what is required though, for evolution studies?
I see that you too are uninterested in communication. Why do you bother commenting?
Why? Aren’t the lengths of the branches proportional to the amount of mutations? Perhaps a good study would connect L0 to A0, right?
See, that’s you presenting claims. You need to stop. In order to interpret a branch length as a number of mutations in some time period, or to compare the number of mutations over time (i.e. mutation rate) between branches, you need to have a root. If the root, for example, is in the middle of branch L0, then it doesn’t have a high mutation rate.
I’ve also been tacitly agreeing with your implicit claim that the tree shows numbers of mutations at all, when what it really shows is numbers of substitutions, i.e. mutations that have made it into the terminal taxa (presumably individuals). Most mutations, of course, will have disappeared along the way. The substitution rate equals the mutation rate only if loci are evolving neutrally. Do you think they are?
The starburst pattern isn’t a polytomy, but polytomies have been noted on the Y-chromosome, and are consistent with the some of the features of the pattern, for example:
You can see H and G on Carter’s starburst graph generated by MEGA.
From Carter’s paper:
Independent of the citation of Rupe and Sanford, there are other secular papers that support “most new mutations will be lost to drift.”
Carter points out:
Ok, so what if there is correlation between L0 (roughly speaking the female line) and A0 (the male line), what would explain that. Would you expect that to from from a founding population of 10,000, or is that more consistent with a nice tight bottleneck?
Btw, John Harshman, would you expect polytomies to be more consistent with a bottleneck or a founding population of 10,000 individuals. Any guesses on the population structure that makes polytomies?
According to Larry Moran’s estimates human mutation rate is 130 mutations per generation…
http://sandwalk.blogspot.com/2015/04/human-mutation-rates-whats-right-number.html
How do you know what Adam and Eve’s mutation rate was? How about after the the “bottleneck” of the Noah’s flood?
Is there some solid proof to support one side of the argument over the other other than pure speculations both of which are based on evolutionary assumptions?
That’s funny, you don’t have one yourself.
Last I checked, physical entities can’t be spoken, or “willed”, or “thought”, or “wished” into existence. And thus the quintessential double standard upon which creationism rests is revealed.
Not to mention that it’s essentially just god-of-the-gaps reasoning.
I don’t know, right now I think the issues are jello, and we’re hoping they get solidified.
Right now the issue is the bottleneck. John Harsham says there was no bottleneck, that is the human ancestral population was always above some number (like 10,000, since he assumes they evolved from ape-like ancestors).
I am asking whether, given Carter’s graphs and the evidence of polytomies and the rest of the data from Carter’s paper whether John Harshman is going to stick to his position.
So I asked him, if there exists a polytomy, does that suggest the ancestors of a branch were a large or small population? OK, next question, given that we find polytomies, how close are the polytomies in relation to that center of the starburst pattern. He says the starburst pattern is a graphical illusion of unrooted trees. I countered by saying “don’t the branch lengths represent the amount of mutations”?
Harshman argues against bottle neck, I argue for. Bottle necks suggest adam and eve and Noah.
The kicker… bwhaha! What if we get the starburst pattern for all mammals. How’s John Harshman going to explain that? Ah, yes, now we have a testable prediction.
When you say “starburst pattern” what do you mean? When you say “center of the starburst pattern” what do you mean? Does it not make you just a little bit uncomfortable to make these pronouncements on a subject that you also admit yourself to be entirely ignorant of?
Gee John, when I start to make a point, you pretend like what I’m saying is idiosyncratic. Well, you can go to this link:
https://evolution.berkeley.edu/evolibrary/news/160505_treeoflife
So why are pretending you don’t understand what I’m saying. It’s not like the “starburst pattern” has been mentioned elsewhere. The “starburst pattern” phrase is on an elementary education website, surely by now you’ve encountered it? I guess not. So you can thank me for teaching you some elementary evolutionary biology if you’ve not encountered “starburst pattern” before.
See what I mean about your arrogance on subjects you know nothing about? The actual point about that quote is that the pattern you see isn’t real; it’s just, as even that site says, an arbitrary arrangement of branches. And you don’t understand the point of the last, bolded bit of what you quote either; in fact the trees you posted almost certainly do not root at the center. Smug arrogance ill becomes the ignorant. It’s time you realize that.
John,
Do you or do you not see a starburst pattern? Don’t go into “I don’t know what you mean” mode. You deserved to be called out pretending you didn’t understand when you said “what do you mean.”
And do you or do you not know the meaning of the center of the starburst pattern?
That is not my assumption and it seems irrelevant to whether or not there is a real Adam and Eve.
No, Humans and Chimps have a similar phenotype they don’t have a nearly identical phenotype.
None of this seems at all relevant to the topic at hand which is, is there a two person bottleneck when it in comes to human origins?
peace
It really depends on your starting assumptions.
I begin a study of human origins with the presupposition that Adam and Eve must have existed. That much is nonnegotiable.
The question for me is how all that worked.
But there is a reason to doubt this given YEC.
A YEC would say that, that evidence of course must be balanced against other contrary evidence including their own personal experience and eyewitness testimony from a person who was present at humanities’ origin.
peace
I do see a starburst pattern, though in fact I was unfamiliar with the term. Even had I known, I wouldn’t have known what you meant by it, and your answer suggests that you attributed some real significance to it rather than it being just a graphic style.
Anyway, the center means nothing, as your source itself said. You apparently disagree, but on what basis?
No, it’s relevant, because if there is common descent then shared alleles are evidence.
Not relevant. Why should certain MHC alleles be preferentially more similar to human alleles than the typical alleles at the typical locus?
That’s because you don’t understand the argument. Do you need to have it explained?
Evidence of what?? The lack of a bottleneck??
Off the top of my head I would speculate that it’s because these alleles correlate with places where humans and chimps are more similar than is typically the case.
Again this does not seem to be at all relevant.
Humans and Chimps could be very closely related and descended from a common ancestor and there still be a bottle neck of two at the origin of our species.
Just to be clear for the record.
I don’t buy the idea that genetic isolation is what defines a species or it’s boundaries. That seems to be an unsupported assumption.
peace