Two-million-year-old Adam and Eve still possible: Dr. Ann Gauger’s model remains viable

A few weeks ago, I wrote a short post titled, Adam and Eve still a possibility?, in which I drew readers’ attention to the work of geneticist Richard Buggs, Reader in Evolutionary Genomics at Queen Mary University of London, who thinks it’s still theoretically possible that the human race once passed through a short, sharp population bottleneck of just two individuals, followed by exponential population growth. Biologist Dennis Venema, professor of biology at Trinity Western University in Langley, British Columbia, has recently written a two-part reply to Buggs, titled, Adam, Eve and Population Genetics: A Reply to Dr. Richard Buggs (Part 1) and A Reply to Dr. Richard Buggs (Part 2). But in a comment in response to a query of mine, Professor Venema conceded that at the present time, science cannot rule out Dr. Ann Gauger’s hypothesis that there was a severe bottleneck around two million years ago, with the emergence of Homo erectus, whom she identifies as the first true human being. When I pressed Professor Venema, saying, “In plain English, what you’re saying is that science can’t rule out an original couple, if they lived more than 1 million years ago,” he replied:

I guess it depends on how reliable you think PSMC methods are as they approach this time frame. The data looks smooth to me out to around 1.5 MYA or so, plus or minus, but the method loses its power as you go back further and further.

In a recent email message, Dr. Gauger clarified her position on Adam and Eve:

I did not settle on an old age for Adam so that the population genetics would work out or because I was seeking to prove two progenitors. It was because I could not understand why God would create Homo species so close to us and not be part of us, and because of morphology. I find species definitions to be tricky things, and sometimes they are assigned because of an agenda. H ergaster and H habilis are disputed for example. But for me Turkana boy is clearly human.

So I arrived at an early date because paleontology. I am aware of arguments for 200k (first modern skeleton), 70 k (Blombos cave, migration out of Africa), or 20-10k to match Genesis.) We will see if any of these dates, as well as the older one, can accommodate a unique origin based on AFS, LD, and several other pop gen statistics. Feel free to pass this on.

Dr. Gauger has adduced evidence that Homo erectus and Homo ergaster (African Homo erectus) were rational beings, who were capable of foresight: they transported tools over distances of 12-13 kilometers, compared to distances of just tens or hundreds of meters for Australopithecus and early Homo (see here). In addition, there is evidence (see also here) that Homo ergaster was able to tame fire as far back as 1,000,000 years ago, and perhaps use it to cook meat as well, although Wil Roebroeks of Leiden University in the Netherlands and Paola Villa, a curator at the University of Colorado Museum of Natural History in the U.S., cautions that we don’t have evidence of regular fire use going back any further than 400,000 years ago. Finally, excavations at the South African site of Kathu Pan suggest that Homo ergaster had a sense of aesthetics. As Dr. Gauger describes it:

…[T]he site has yielded what is termed, the ‘Master Hand-Axe’ which dates to approximately 750 000 BP rendering it the oldest artifact which is indisputably aesthetic i.e. worked for beauty and symmetry, perfectly oriented, and worked considerably beyond the functional requirements of the hand-axe, which could have been achieved with half or fewer blows (see Figure 4-2). The technology which produced it is known as the Acheulian, and the artifacts are thought to be made by Homo ergaster (Homo erectus in Africa), a diverse grouping of early humans commonly imagined as small-brained, small-jawed and robustly built, with heavy eyebrow ridges.

When I look at that master handaxe, I see aesthetics, painstaking care, and a joy in the materials. I see mind.

In a recent comment on Biologos, I expressed reservations about Dr. Gauger’s ancient Adam and Eve scenario:

However, if I were to identify the chief flaw of the ancient Adam and Eve scenario, it would be this: modern human behavior doesn’t appear until 100,000 years ago. Homo erectus may have had foresight (transporting tools over distances of more than 10 kilometers), the ability to control fire (although this is hotly disputed) and even a sense of aesthetics (judging from the elegance of some Acheulean tools), but it almost certainly lacked the capacity for art, religion and science. This means that in some ways it was less human than we are – which means that if we are to believe in Adam and Eve, we have to give up belief in human equality.

It is instructive to compare Homo erectus with modern-day tribes whose lifestyle has been described by some as “primitive.” Members of these tribes have relatively little trouble in adapting to the cognitive demands of civilization, some making the transition in as little as a generation. I doubt very much whether Homo erectus could have done that. And I also doubt whether anyone could have preached the Gospel to Homo erectus.

Finally, in a recent post on The Skeptical Zone, I marshaled evidence indicating that Homo erectus almost certainly lacked the use of language, and that even the Neandertals probably lacked it. What’s more, the human brain appears to have evolved specific traits in the lineage leading to Homo sapiens, which allowed our species to possess a full-blown theory of mind and imagine what others were thinking about them.

For her part, Dr. Gauger is not troubled by the fact that Homo erectus lacked our level of linguistic ability. And in a post on Biologos, she responded as follows to my concerns about the lack of symbolic culture in Homo erectus: “First of all, our full capacity for art, drama, philosophy, religion and language was not present 300,000 years ago. Nor was it present, it could be argued until the Egyptians, the early Greeks, and the Chinese had their cultural flowering.” I agree with Dr. Gauger that early Homo sapiens, who lived 300,000 years ago, lacked “our full capacity for art, drama, philosophy, religion and language.” I think that these abilities appeared 100,000 years ago, with the emergence of modern human behavior (see also here). Dr. Gauger argues that the long lag between the appearance of Homo sapiens and the emergence of behavioral modernity means that we shouldn’t consider Homo erectus subhuman because it didn’t behave in this way. I would argue, however, that the human brain did not stop evolving with the appearance of Homo sapiens. It may have subsequently acquired the traits which enabled us to use language and to possess a full-blown theory of mind.

So the long and the short of it is: Dr. Gauger’s model of a two-million-year-old Adam and Eve remains scientifically viable, but their minds would have been very different from ours. Personally, I wouldn’t call Homo erectus a true human being. The Neandertals I’m not so sure about, for reasons I’ve discussed previously.

I’ll just finish by mentioning the work of Dr. Joshua Swamidass, who is an assistant professor at Washington University in Saint Louis where he runs a computational biology group. In an article titled, A Genealogical Rapprochement on Adam?, he accepts “the genetic evidence in which it appears (1) our ancestors arise as a population, not a single couple, and that (2) we share ancestry with the great apes,” but also proposes that an individual named Adam “was created out of dust, and Eve out of his rib, less than 10,000 years ago in a divinely created garden where God might dwell with them, the first beings with opportunity to be in a relationship with Him.” After leaving the Garden, Adam and Eve’s offspring blended with that of their neighbors in the surrounding towns. “In this way, they became genealogical ancestors of all those in recorded history. Adam and Eve, here, are the single-couple progenitors of all mankind.” Of course, humans today have many genealogical ancestors, not just Adam and Eve. An article outlining Dr. Swamidass’s hypothesis will appear in the March 1, 2018 issue of PSCF (Perspectives on Science and Christian Faith). The important thing for readers to grasp is that genealogical ancestry is not genetic ancestry: “Though scientific discourse focuses on genetic ancestry, genealogical ancestry is germane to the theological claims about Adam.” Adam and Eve are ancestors of us all, because genealogical ancestry becomes universal in just a few thousand years. Dr. Swamidass contends that “Scripture and theology, at most, make claims about genealogical ancestry, but not genetic ancestry,” because when Scripture was written, people had no notion of what genes were. I’m not sure, however, that it’s that simple. The Bible appears to affirm that Adam and Eve were the only genealogical ancestors of the entire human race. As Acts 17:26 puts it: “From one man he made all the nations, that they should inhabit the whole earth; and he marked out their appointed times in history and the boundaries.” I’m also not sure exactly what new trait Adam and Eve were supposed to have possessed, under the scenario proposed by Dr. Swamidass, since he explicitly declares that even the human beings living outside Adam and Eve’s Graden were made in the image of God. It seems the only thing that was genuinely new about Adam and Eve was that they were spiritually fallen. But because genetic information is transmitted only unreliably, Dr. Swamidass argues that Adam and Eve, if they existed, “probably did not transmit DNA to all their descendants, nor did they transmit any identifiable DNA to any of their descendants.” He continues: “This means that Adam and Eve’s DNA is not how the Fall or original sin, if they exist, is transmitted to all of us.” At any rate, Dr. Swamidass’s article is a very stimulating read, which is sure to take the Adam and Eve debate in a new direction.

I’d now like to throw the discussion open to readers – especially those with a Christian background. If you had your druthers, which Adam and Eve would you pick? A two-million-year-old one, who was perhaps a lot dimmer than us, as proposed by Dr. Gauger? Or a Neolithic one, as proposed by Dr. Swamidass, who interbred with other humans that were made in God’s image and likeness, and left descendants all over the globe? Or neither of the above?

I’ll leave you all with a concluding thought: “We are more different genetically from people living 5,000 years ago than they were different from Neanderthals,” according to John Hawks, a professor of anthropology at the University of Wisconsin-Madison. Many of the genetic mutations that have spread through the human population in the last few thousand years relate to “changes in the human diet brought on by the advent of agriculture, and resistance to epidemic diseases that became major killers after the growth of human civilizations.” Civilization seems to have been what’s changed us most. But how has it changed our brains? That I don’t know. Maybe someone can tell me. Over to you.

300 thoughts on “Two-million-year-old Adam and Eve still possible: Dr. Ann Gauger’s model remains viable

  1. Flint: In Paul’s day, claims of direct-to-the-brain revelation were regarded as dispositive, easily trumping direct observation.

    No one said anything about any direct-to-the-brain revelation?

    The revelation I’m talking about is common to everyone and is accessible to direct observation (what ever that is)

    peace

  2. Joe Felsenstein: So we have a case of inheritance, only not a documented case, nor one that can be checked by looking in families of present-day people.

    No one said it was not documented and no one said it could not be checked out.

    Just to head off any misunderstanding I would fully expect that the differences are empirically evident.

    I only said that I don’t believe they are entirely genetic.

    Can you really not conceive of the possibility of real differences that are not entirely reducible to genes?

    peace

  3. fifthmonarchyman: If you all are intrested here is an article about 2 phenotypicaly distinct species of redpoll that are genetically identical

    Perhaps you can look up “identical” in that dictionary of yours.

  4. Corneel: Perhaps you can look up “identical” in that dictionary of yours.

    quote:

    They found no DNA variation that distinguishes Hoary Redpolls from Common Redpolls. Furthermore, another redpoll species found in Europe—the Lesser Redpoll—also had extremely similar DNA sequences. This extreme similarity among all the redpolls stands in marked contrast to studies of other groups of birds—such as Black-capped and Carolina Chickadees—which show differences at many regions of the genome.

    end quote:

    from the article

    peace

  5. fifthmonarchyman,

    The authors themselves phrase that slightly differently.:

    Expanding upon previous findings, we present evidence of (i) largely undifferentiated genomes among currently recognized species; (ii) substantial niche overlap across the North American Acanthis range; and (iii) a strong relationship between polygenic patterns of gene expression and continuous phenotypic variation within a sample of redpolls from North America. The patterns we report may be caused by high levels of ongoing gene flow between polymorphic populations, incomplete lineage sorting accompanying very recent or ongoing divergence, variation in cis-regulatory elements, or phenotypic plasticity, but do not support a scenario of prolonged isolation and subsequent secondary contact.

    “Undifferentiated” does not equal “identical”. Also, note the variation in cis-regulatory elements part: they did not exclude a genetic basis fot the phenotypic differences

  6. Corneel: “Undifferentiated” does not equal “identical”.

    OK if you want to split hairs. Usually if there is no difference between two things we call them identical. But I have no problem if you want to quibble

    Corneel: they did not exclude a genetic basis fot the phenotypic differences

    I’m not excluding a genetic basis either I’m just not demanding it

    peace

  7. Corneel,

    thank you for reading the article

    Suppose humans and hypothetical “others” were like the species of redpolls

    Would we be able with our current genetic understanding to tell them apart with out looking at phenotype?

    peace

  8. fifthmonarchyman: I only said that I don’t believe they are entirely genetic.

    Can you really not conceive of the possibility of real differences that are not entirely reducible to genes?

    Sure — I said that there are lots of differences that are due to direct effects of environment on the phenotype.

    But in that comment I also said that the issue here is not differences of phenotype but inheritance of the differences.

    fifthmonarchyman: Epigenetics perhaps

    Are you aware that existing epigenetic mechanisms have not been observed to have inheritance for more than two or three generations?

    So where we are is this: you are talking about an undefined phenotype, inherited by an unknown mechanism, new to science. And you are arguing that it explains the influence of two hypothetical people on all of us. And when anyone says that this is a nonexplanation, you demand that they get into a big argument with you about the definition of species.

    Whereas what I’m pointing out is that even if we allow you your very own definition of species, that would not solve the problem.

  9. fifthmonarchyman: thank you for reading the article

    no problem

    fifthmonarchyman: Suppose humans and hypothetical “others” were like the species of redpolls

    Would we be able with our current genetic understanding to tell them apart with out looking at phenotype?

    You seem to be missing the point. The redpoll morphs are not “species” since they are interbreeding and continuous gene flow is the most parsimonuous explanation for the lack of differentiation between them. If I were to guess, I’d say that the phenotypic differences have a genetic basis like say hair colour in humans. So we are still looking for a way how your “human” trait gets passed through evolutionary time by non-genetic means.

  10. Joe Felsenstein: Whereas what I’m pointing out is that even if we allow you your very own definition of species, that would not solve the problem.

    God’s definition of species as He has shared with fifth

  11. Joe Felsenstein: Are you aware that existing epigenetic mechanisms have not been observed to have inheritance for more than two or three generations?

    From what I understand we did not know of any epigenetic mechanisms at all that had inheritance until a few years ago.

    That did not mean that they did not exist it only meant that we had not discovered them

    Joe Felsenstein: So where we are is this: you are talking about an undefined phenotype, inherited by an unknown mechanism, new to science.

    Allow me to speculate a little bit just for fun. This is just a couple of possibilities out of many

    Lets say the phenotype is language.

    The critical period hypothesis implies that language would not arise in the human species until the appropriate environmental stimuli was present even if the genetic basis for language was present.

    One the appropriate verbal stimuli occurred humans would pass language on to their offspring culturally rather than genetically.

    If this speculation is correct Adam became human when he was taught language at a young age.

    Here is another possible mechanism suppose the phenotype in question is undefined but it arose when Eve’s body interacted with a new species of gastrointestinal microbiota to form a symbiotic relationship similar to lichens.

    The biota would then be passed on to Eve’s offspring in perpetuity.

    The point of all this is speculation is not to say what happened it’s to illustrate that there is simply no reason to exclude extra-genetic mechanisms.

    Of course what makes us human might turn out to be entirely genetic I just think it’s not necessary to limit ourselves in this way

    Joe Felsenstein: Whereas what I’m pointing out is that even if we allow you your very own definition of species, that would not solve the problem.

    What problem would it not solve? The problem is the impossibility of A&E given the hypothetical existence of a genetic population of 10 thousand.

    It seems to me that abandoning the whacked out idea that a species required genetic isolation solves that problem nicely.

    peace

  12. Corneel: The redpoll morphs are not “species” since they are interbreeding

    You are assuming with out evidence that the “biological concept” is an accurate determiner of what a species is.

    The fact is redpolls have very distinct phenotypes and have been recognized as separate species by ornithologists for a over a hundred and fifty years.

    The only reason to abandon that common sense intuition that they are indeed separate species is continued slavish obedience to a whacked out definition.

    peace

  13. newton: God’s definition of species as He has shared with fifth

    God does not have to personally share his definition of species for us to that the biological species concept is whacked.

    All we have to do is look around to see that

    peace

  14. fifthmonarchyman: The fact is redpolls have very distinct phenotypes and have been recognized as separate species by ornithologists for a over a hundred and fifty years.

    Good grief, do you actually read your own links:

    If Hoary and Common Redpolls had long been separate species, then the birds sampled should have mostly fit neatly into two categories, both by visual appearance and genetically. Instead, there were a few birds that definitely fit the visual description of what we call a Common Redpoll, a few birds that definitely fit the pattern for a Hoary Redpoll, and a lot of birds in the middle—with varying degrees of whitish breast and faint brown streaks.

  15. fifthmonarchyman: Corneel: “Undifferentiated” does not equal “identical”.

    OK if you want to split hairs. Usually if there is no difference between two things we call them identical. But I have no problem if you want to quibble

    Just want to clarify this, because it annoys me that I am being accused of splitting hairs, whereas this is a fundamental difference. If the two species (or morphs or whatever) were genetically identical, that would mean there were no genetic polymorphisms and we would in fact be looking at a clonal population. I hope you agree this is quite different from what has been reported.

  16. Corneel: Good grief, do you actually read your own links:

    Yes, I present articles to share the facts contained in them not to endorse the opinions expressed

    The sunfish in my pond have a similar distribution as redpolls.

    There are a few fish that have a distinctive Lepomis cyanellus phenotype and a few that have a Lepomis macrochirus phenotype and a good number of fish that would fit somewhere in between what is seen as typical for the two species.

    That is no surprise we see the same thing with all most all species at the edges we see an admixture of traits.

    Coyotes and wolves spring quickly to mind. That does not mean that Coyotes and Wolves are one species or Green sunfish and blue gill don’t exist.

    It simply means that closely related individuals interbreed in the wild and there are no genetically isolated populations.

    Which is another reason we should dump the biological concept of species as I have been saying all along.

    peace

  17. Corneel: Just want to clarify this, because it annoys me that I am being accused of splitting hairs

    I did not mean to annoy

    Corneel: If the two species (or morphs or whatever) were genetically identical, that would mean there were no genetic polymorphisms and we would in fact be looking at a clonal population.

    I never intended to imply all redpolls were clones.

    I simply meant to express the fact that there was no discernible genetic difference between the two different species.

    I thought that was obvious in that I was comparing the species of redpolls to humans verses hypothetical closely related Homo individuals that might have existed at the time of A&E.

    I’m sorry you missed that

    peace

  18. fifthmonarchyman: Coyotes and wolves spring quickly to mind. That does not mean that Coyotes and Wolves are one species or Green sunfish and blue gill don’t exist.

    Hm hm, these are all genetic differences. We were looking for a non-genetic method of inheritance that would sustain a phenotypic trait (“being human”) in evolutionary time, remember? Will you concede that the Redpoll example does not support that argument?

    After that, we can discuss your theory that “being human” is determined by gastrointestinal biota.

  19. fifthmonarchyman: I simply meant to express the fact that there was no discernible genetic difference between the two different species.

    I thought that was obvious in that I was comparing the species of redpolls to humans verses hypothetical closely related Homo individuals that might have existed at the time of A&E.

    I’m sorry you missed that

    No, you implied that the phenotypic differences could not possibly be caused by a genetic difference because the morphs were “genetically identical”. This is just wrong.

    I did not miss that.

  20. fifthmonarchyman: God does not have to personally share his definition of species for us to that the biological species concept is whacked.

    Two points,

    First ,did He personally reveal a definition to you?

    Second, if there is not some way to absolutely know God’s definition of a biological species or of IPhones then the problem you have with defintions remains

    All we have to do is look around to see that

    Pretty sure that is what biologists do for a living. People have different viewpoints.

    peace

  21. newton: Pretty sure that is what biologists do for a living. People have different viewpoints.

    When pressed, filthy told me that we have to observe genotypes and phenotypes and make our case. I am writing an article right now to let those materialist scientists know this insight that could only come from filthy and his (or her) non-materialistic rich metaphysics (with the proper attribution, of course).

    Because, you know, nobody does that. Their materialism doesn’t allow them to think, “hey, maybe if I look at these things, like phenotypes and genotypes. and study them across what looks like a coherent population, and then try and make sense of them in terms of, say ecology, role of some population in an ecosystem, or this or that, we might learn something new …”

    Nope. We needed filthy to come and tell us.

  22. fifthmonarchyman: Here is another possible mechanism suppose the phenotype in question is undefined but it arose when Eve’s body interacted with a new species of gastrointestinal microbiota to form a symbiotic relationship similar to lichens.

    The biota would then be passed on to Eve’s offspring in perpetuity.

    Wow, so that’s why we’re human! Would certainly make you think twice before you took any antibiotics, or consumed any probiotic yoghurt.

  23. Corneel: Hm hm, these are all genetic differences.

    Yes and we see the same effect in redpolls with out any genetic differences.

    Corneel: Will you concede that the Redpoll example does not support that argument?

    No
    We can see the same sort of divergences in a genetically “undifferentiated” population as we do in common differentiated ones.

    That pretty much confirms my argument. Don’t you agree?

    Corneel: After that, we can discuss your theory that “being human” is determined by gastrointestinal biota.

    It’s just a fun speculation and we are talking about the interaction between hominid genome and that of the particular biota. Not the microbes on their own.

    I’m not sure why you would exclude the possibility out of hand.

    We do know “being panda” is determined by an interaction with it’s gastrointestinal biota and this relationship has been maintained with out genetic inheritance since the time of the dinosaurs so I see no reason assume such a thing is impossible.

    https://www.sciencedaily.com/releases/2017/12/171206122451.htm

    check this out

    quote:

    The bacterial microbiota in the gut helps normal brain development, says Cryan. “If you don’t have microbiota you have major changes in brain structure and function, and then also in behaviour.”

    end quote:

    from here

    http://www.bbc.com/future/story/20140221-can-gut-bugs-make-you-smarter?ocid=fbfut

    peace

  24. Joe Felsenstein: Would certainly make you think twice before you took any antibiotics, or consumed any probiotic yoghurt.

    If we killed the gut microbes in a panda that allowed it to digest bambo it would quickly kill the animal.

    If we did it to all Pandas the entire species would go extinct in short order. I see no reason to exclude the possibility that there is not some as yet hidden symbiotic organism with a possibly similar role sharing our space.

    http://science.sciencemag.org/content/330/6012/1768

    We could not call something that eliminated an organism like that antibiotic we would call it deadly poison and we all would be wise to avoid it

    peace

  25. Entropy,

    Is there a reason that you are so grumpy?

    I merely suggested we abandon a faulty definition. I did not insult your girl friend.

    Entropy: Because, you know, nobody does that.

    I never said nobody does that. I said that we would be better off if we abandoned an antiquated incorrect definition of species. Many scientists have already done that those that haven’t are increasing putting less emphasis on that biological species concept.

    I just wish they would hurry up in that regard.

    You would think I stole Christmas 😉

    peace

  26. fifthmonarchyman: We could not call something that eliminated an organism like that antibiotic we would call it deadly poison and we all would be wise to avoid it

    If the organisms were responsible for us being human, getting rid of them might or might not kill us, but it would remove our humanity. Quite a large effect.

  27. Joe Felsenstein: If the organisms were responsible for us being human, getting rid of them might or might not kill us, but it would remove our humanity. Quite a large effect.

    something like this perhaps 😉

    quote:
    Of all the things I’ve lost I miss my mind the most.
    end quote:
    Ozzy Osbourne 😉

    peace

  28. Joe Felsenstein,

    seriously though. I would expect that we are much more at risk of loosing our humanity by what we try to gain than what we might accidentally loose

    quote:

    For what will it profit a man if he gains the whole world and forfeits (looses) his soul? Or what shall a man give in return for his soul?
    Matt 16:26

    end quote:

    peace

  29. Joe Felsenstein: If the organisms were responsible for us being human, getting rid of them might or might not kill us, but it would remove our humanity. Quite a large effect.

    Sounds like a lot of Trump voters lost their organisms.

  30. fifthmonarchyman: seriously though. I would expect that we are much more at risk of loosing our humanity by what we try to gain than what we might accidentally loose

    Does only the good stuff count as humanity, maybe the organisms are making us bad .

  31. fifthmonarchyman: We can see the same sort of divergences in a genetically “undifferentiated” population as we do in common differentiated ones.
    That pretty much confirms my argument. Don’t you agree?

    No, because the phenotypic differences between the morphs most likely have a solid genetic basis. You simply misinterpret what undifferentiated means. It does not mean genetically identical.

    But we have been through this …

  32. Corneel: No, because the phenotypic differences between the morphs most likely have a solid genetic basis.

    The study found some possible difference in non coding DNA. Thus it might be relevant to epigenetic activity. However the part used to create proteins (the genes) was found to be undifferentiated.

    Corneel: But we have been through this …

    I would have thought so.

    peace

  33. newton: Does only the good stuff count as humanity, maybe the organisms are making us bad .

    I’m not sure how it’s inherited but the “total depravity” part most certainly is a bad part of being human.

    peace

  34. fifthmonarchyman: The study found some possible difference in non coding DNA.

    Where does it say that?

    fifthmonarchyman: Thus it might be relevant to epigenetic activity.

    What? How so?

    fifthmonarchyman: However the part used to create proteins (the genes) was found to be undifferentiated.

    OK. I am calling bullshit on this. Where did you get this from?

  35. Corneel: Where does it say that?

    from the very paragraph you posted

    quote:

    The patterns we report may be caused by high levels of ongoing gene flow between polymorphic populations, incomplete lineage sorting accompanying very recent or ongoing divergence, variation in cis-regulatory elements

    end quote

    cis-regulatory elements are:

    quote:

    Cis-regulatory elements (CREs) are regions of non-coding DNA which regulate the transcription of neighboring genes.
    end quote:

    from here

    https://en.wikipedia.org/wiki/Cis-regulatory_element

    Cis-regulatory elements are implicated in Epigenetic changes

    quote:

    “We brought together the cis (within DNA sequence) and trans (acting on a DNA sequence) factors to show how Polycomb targets specific PREs and broadly regulates plant gene expression,” Wagner said. “This is the first demonstration that this mechanism — recruitment of Polycomb by these signposts in the DNA — acts in species outside of fruit flies. In the future I could use these motifs to epigenetically enhance desireable traits such as yield or drought tolerance without significantly changing the coding sequence.”

    end quote:

    from here

    https://phys.org/news/2017-08-biologists-genes-dont.html

    peace

  36. fifthmonarchyman: I’m not sure how it’s inherited but the “total depravity” part most certainly is a bad part of being human.

    peace

    So it was not a Fall ,it was from God’s own hand the evil in man springs. Nice

  37. fifthmonarchyman,

    Fifth, you misunderstood. The study did not examine cis-regulatory elements. They just hypothesized, just like me, that there must be specific genetic factors responsible for the morphological differences.

    Let me emphasize that: cis-regulatory elements are binding motifs in the DNA. They are genetic, not epigenetic.

    As for the quote you dug up:

    fifthmonarchyman: “We brought together the cis (within DNA sequence) and trans (acting on a DNA sequence) factors to show how Polycomb targets specific PREs and broadly regulates plant gene expression,” Wagner said. “This is the first demonstration that this mechanism — recruitment of Polycomb by these signposts in the DNA — acts in species outside of fruit flies. In the future I could use these motifs to epigenetically enhance desireable traits such as yield or drought tolerance without significantly changing the coding sequence.”

    I am sorry but this is completely irrelevant. What on earth do Polycomb group proteins have to do with different morphs in Redpolls? You just saw “epigenetics” in relation to cis-regulatory elements and assumed that it somehow supported your position. No, it doesn’t. Lots of proteins are capable of binding DNA motifs and the genetic variation in those elements is supposed to be an important substrate for morphological evolution. It even says so in the wikipedia page you linked to:

    CREs have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression.[3] Mutations arising within a CRE can generate expression variance by changing the way TFs bind. Tighter or looser binding of regulatory proteins will lead to up- or down-regulated transcription.

    Yes, mutations. Good ol’fashioned genetic mutations.

  38. Corneel: The study did not examine cis-regulatory elements. They just hypothesized, just like me

    I did not mean to imply that they specifically studied cis-regulatory elements I meant to point out that what the saw was entirely consistent with differences in cis-regulatory elements

    Corneel: Let me emphasize that: cis-regulatory elements are binding motifs in the DNA. They are genetic, not epigenetic.

    On this I would strongly disagree. cis-regulatory elements are genetic only if you define genetic to mean anything composed of DNA.

    It’s not a gene if it does not code for a protein

    quote:
    Genes, which are made up of DNA, act as instructions to make molecules called proteins.
    end quote:

    from here

    https://ghr.nlm.nih.gov/primer/basics/gene

    cis-regulatory elements don’t act as instructions to make proteins by definition they regulate the work of genes.

    The reason that the biologists considered redpolls to be genetically undifferentiated is because the actual genes (elements that code for proteins) were undifferentiated.

    If you want to include everything that influences the production of proteins in your definition of “genetic” then literally everything is genetic including the environment.

    I am using the definition of genetic that the biologists looking at red polls and early human populations are using namely those things that “act as instructions to make proteins”.

    Corneel: Yes, mutations. Good ol’fashioned genetic mutations.

    If you think that all mutations are “genetic” then we are talking past each other here.

    On the bright side it has helped us clarify.

    Let me be explicit.

    When I say that i do not necessarily expect to see any genetic difference between humans and hypothetical “others” I am talking about actual genes

    Of course I assume that there were differences in gene expression between the two groups.

    How could there not be?

    I hope that helps

    peace

  39. fifthmonarchyman: On this I would strongly disagree. cis-regulatory elements are genetic only if you define genetic to mean anything composed of DNA.

    Eh, right. or RNA. Which is exactly what all geneticists do …

    fifthmonarchyman: It’s not a gene if it does not code for a protein

    quote:
    Genes, which are made up of DNA, act as instructions to make molecules called proteins.
    end quote:

    I thought you preferred the Merriam Webster dictionary:

    a specific sequence of nucleotides in DNA or RNA that is located usually on a chromosome and that is the functional unit of inheritance controlling the transmission and expression of one or more traits by specifying the structure of a particular polypeptide and especially a protein or controlling the function of other genetic material

    fifthmonarchyman: The reason that the biologists considered redpolls to be genetically undifferentiated is because the actual genes (elements that code for proteins) were undifferentiated.

    Bzzt, wrong, it is because they failed to find significant allelic differences at restriction site polymorphisms and SNPs.

    fifthmonarchyman: If you want to include everything that influences the production of proteins in your definition of “genetic” then literally everything is genetic including the environment.

    I don’t. I include everything made of DNA or RNA. That includes regulatory elements.

    fifthmonarchyman: I am using the definition of genetic that the biologists looking at red polls and early human populations are using namely those things that “act as instructions to make proteins”.

    They are not using that definition.

    fifthmonarchyman: If you think that all mutations are “genetic” then we are talking past each other here.

    We are talking past each other because you seem to think that mutations of DNA sequences do not qualify as “genetic”

  40. I’m in a hurry

    just came across an interesting example of using CRISPR to alter the activity, rather than the underlying sequence, of disease-associated genes.

    https://www.sciencedaily.com/releases/2017/12/171207141735.htm

    quote:

    the researchers increased the expression of genes in the same pathway as the mutated gene, over-riding the effect of the damaged gene. “We are not fixing the gene; the mutation is still there,” says Belmonte, “Instead, we are working on the epigenome and the mice recover the expression of other genes in the same pathway.

    end quote:

    will talk more later

    😉

    peace

  41. Corneel: I don’t. I include everything made of DNA or RNA. That includes regulatory elements.

    from the article

    quote:

    They used another AAV virus to introduce a short single guide RNA (sgRNA),

    and

    . “We are not fixing the gene; the mutation is still there,” says Belmonte, “Instead, we are working on the epigenome

    end quote;

    peace

  42. fifthmonarchyman,

    I am familiar with the technique. What presently escapes me is how this is going to be relevant to differentiation among red polls or the transmission of “humanity” by A&E. Remember: the epimutations need to be stable for several hundreds or thousands of generations.

    I eagerly await your explanation.

  43. Corneel: What presently escapes me is how this is going to be relevant to differentiation among red polls or the transmission of “humanity” by A&E.

    We detoured from the conversation about A&E a while back. Right now we are on the tangent of whether something like changes made to RNA that regulates the expression of genes is epigenetics or not.

    You seem to be saying that it’s not I and would disagree.

    I think that the authors of the study agree with me

    again

    quote:
    “We are not fixing the gene; the mutation is still there,” says Belmonte, “Instead, we are working on the epigenome
    end quote:

    Corneel: Remember: the epimutations need to be stable for several hundreds or thousands of generations.

    1) I have no idea of how many generations we are talking about but it could be relatively few depending on the assumptions we start with.

    2) Just because we have no idea how epigenetic changes can persist over the long term is no reason to reject the possibility that they can out of hand.

    2) We know that the microbiota that makes the Panda’s existence as a species possible has persisted for millions of years.

    3) It could turn out that there is no possible way for Epigenetic inheritance to persist over the long term and it would not effect the possibility of A&E in the slightest. It would only mean that my fun speculations here are wrong

    peace

  44. fifthmonarchyman: We detoured from the conversation about A&E a while back. Right now we are on the tangent of whether something like changes made to RNA that regulates the expression of genes is epigenetics or not.
    You seem to be saying that it’s not I and would disagree.

    “changes made to RNA” is way too vague for me to agree or disagree to. Let me be specific here: genetic changes are modifications of the nucleotide sequence of DNA, and in some peculiar cases like retroviruses, RNA.

    Some changes to the DNA can be epigenetic though, as long as they do not affect the nucleotide sequence. The best known example is the addition of a methyl group to a cytosine residue (DNA methylation).

    You were arguing that mutations of regulatory elements do not qualify as genetic changes, because these elements are not coding for a polypeptide. That is simply wrong.

  45. fifthmonarchyman: 1) I have no idea of how many generations we are talking about but it could be relatively few depending on the assumptions we start with.
    2) Just because we have no idea how epigenetic changes can persist over the long term is no reason to reject the possibility that they can out of hand.
    2) We know that the microbiota that makes the Panda’s existence as a species possible has persisted for millions of years.
    3) It could turn out that there is no possible way for Epigenetic inheritance to persist over the long term and it would not effect the possibility of A&E in the slightest. It would only mean that my fun speculations here are wrong

    Could you please specify what you mean by “epigenetic inheritance” here? You seem to be happily including both the chromatin modifications in experimental mice models and gut biota. Those are quite different things, and I would like to know what we are discussing.

  46. fifthmonarchyman: 2) We know that the microbiota that makes the Panda’s existence as a species possible has persisted for millions of years.

    We do? *googles* eh nope

    We found that the giant panda gut microbiota is low in diversity and highly variable across seasons. It also shows an overall composition typical of bears and entirely differentiated from other herbivores, with low levels of putative cellulose-digesting bacteria. The gut microbiota of this herbivore, therefore, may not have well adapted to its highly fibrous diet, suggesting a potential link with its poor digestive efficiency.

  47. Corneel: You were arguing that mutations of regulatory elements do not qualify as genetic changes, because these elements are not coding for a polypeptide. That is simply wrong.

    My layman’s understanding has always been that there is a difference between genetics and genomics.

    Genetics deals with genes and genomics deals with the entire structure including things like Cis-regulatory elements. Contrary to what OMagain says I am willing to be educated if I’m incorrect.

    Corneel: Some changes to the DNA can be epigenetic though, as long as they do not affect the nucleotide sequence.

    This is where I’m having difficulty

    in the past I would have assumed that the nucleotide sequence was could be seen as containing two components the coding part and the noncodding part and that when we spoke of genetics we were talking about the coding part.

    I always thought that large parts of the noncoding part is not even conserved over time so could not be a candidate for genetic inheritance.

    Then I remember a few years ago that large sections of ultra-conserved but non-codding DNA could be removed from the genome with no known adverse effects. So this stuff would also seem to not be a candidate for genetic inheritance

    Like I said When I think of genetics I think of genes please explain why this idea is incorrect. articles would be helpful if you know of any

    peace

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