The Great Genetic Bottleneck that Contradicts Ken Ham’s Radical Accelerated Diversification (ie. Post-Flood Hyper-Evolution)

How can a population of organisms reproduce and over time become several hundred species each of which has its own menagerie of characteristics? This is a fundamental evolutionary question for which many different mechanisms have been proposed as solutions over the past 200 years.  With AiG’s Ark Encounter nearing completion Ken Ham is about to put on display his – and AiGs – own understanding of how thousands of species found their origins in a small number of common ancestors.  In other words, he will be more visibly promoting his alternative view of the origin of species that he has been promoting for some time. However, most lay Christians and the general public are likely not familiar with this view I have called radical accelerated diversification. Unfortunately for Ken Ham, the very Ark that he will be promoting as a Christian theme attraction presents the most compelling observational evidence that undermines his own interpretation of the origins of species.

A typical visualization of what happens in a genetic bottleneck. In this case new mutations after the bottleneck begin to increase variation again but that is a very slow process.

A typical visualization of what happens in a genetic bottleneck. In this case new mutations after the bottleneck begin to increase variation again but that is a very slow process.

The problem results form something called a genetic bottleneck.  A genetic bottleneck occurs when the number of individuals in a population is reduced drastically.  Even if this reduction in population is temporary it can have profound lasting effects on the genetic variation in a population.  For example, there is quite a bit of morphological variation among domestic dogs around the world. What if the population of domestic dogs were suddenly reduced to just 20 and they were all Dalmatians? As those Dalmatians reproduce with each other to form larger and larger populations what do you think those dogs would look like?  Yes, Dalmatians.

There could be a million Dalmatians 200 years later. They would have some minor variations but they would all be easily recognized as Dalmatians.  The amount of genetic variation among living Dalmatians is not very great and so future generations would have little genetic variation to work with in terms of allowing them to adapt and change to their environment.  Even if we wished to change them we would have little or no variations to choose from to enact any change over time.  Dalmatians only represent a fraction of the genetic variation present among all dogs but much or most of that variation is lost in a bottleneck event.

Noah’s Ark – genetic bottleneck in the extreme

What would the ultimate genetic bottleneck look like? It would look like a population reduced to only a single reproductive pair that represents an entire species. Does such a bottleneck like this sound familiar?  According to the young earth creationist’ interpretation of scriptures Noah’s flood bottlenecked all living land animals – and apparently plants and fungi too – in the most extreme way possible.  In many cases it reduced species – and they say entire families of species – all the way down to two lone individuals. Population biologists typically get worried about a the genetic health of a species when its numbers get down into the hundreds or even thousands.*  A reduction to just two would be a genetic catastrophe!  Ken Ham is all about global catastrophes but this one would result in the exact opposite result of what he thinks has happened.

Below is a graphic Answers in Genesis has been using the past couple of years to illustrate their view of the origin of species. In this graphic you can see that AiG views “kinds” as diversifying into many species – each represented presumably by thousands or millions of individuals – before Noah’s flood.  The Noahic Flood results in the vast majority of those pre-Flood species going extinct and only a single lineage represented by a single pair of animals is preserved on Noah’s ark. That pair of common ancestors then represents the ancestral stock from which all subsequent species must evolve – yes this is evolution.

The AIG view of the evolution of species within kinds. This is their most recent graphic which they have used to promote their view of the history of life on Earth.

The AIG view of the evolution of species within kinds. This is their most recent graphic which they have used to promote their view of the history of life on Earth. Image from:  https://assets.answersingenesis.org/img/cms/content/contentnode/header_image/speciation.jpg

Ken Ham suggests that all 37 living feline species and 100+ extinct species with their incredible range of features and adaptations were derived from just a single pair of common ancestors?  That variation we see today in felines and the extinct relatives is the results of hundreds of millions of differences in their genomes. Where did this variation come from?

The YEC genetics mantra is that God created “kinds” with huge amounts of variation and that all that evolution mechanisms natural selection does is sort out that front-loaded variation.

Ken Ham tweeted the following today (3/30/2016) in regards to his view of evolution:  Some think natural selection is the same thing as evolution. No. Natural selection works in the exact opposite direction of evolution.

He is not wrong in the sense that strong negative or positive natural selection acts to reduce genetic variation because it eliminates alleles from a population over time. But of course for natural selection to work there must be heritable genetic variation in a population to begin with.  We have observational scientific evidence that species that have been reduced to small population sizes lose their genetic variation and become essentially clones of one another.  As a result, these populations cannot evolve by natural selection or genetic drift and thus will not change until they have replenished their genetic variation.  As long as genetic variation is absent, they do not, and cannot, evolve.

For example, all the cheetahs alive in the world today are nearly genetically identical to each other because that species was bottle necked in the past.  Hundreds of generations later they still haven’t recovered much genetic variation which is only possible via new mutations.  If Ken Ham’s rapid evolution model were correct every species on earth should be as genetically restricted as the cheetahs are but this is not what we observe.  Instead we find that species have a bounty of genetic variation.  Most feline species are more variable than humans and then you have to consider how different species of felines are from one another.

Noah’s ark is the ultimate population, and even species, bottleneck which would have eliminated the vast majority of genetic diversity in all kinds. After departing the Ark these kinds would have been incapable of evolving or diversifying or becoming genetically sorted or whatever term Ken Ham wants to use.  They would look virtually identical today to the way they looked the day they stepped off the Ark.  BTW, this is what we observe. All the animals described in the Bible look and act today they way they are described in the Bible. They have not changed dramatically as the YEC model predicts. Where is their observational evidence that they claim is the only form of real science? I will provide observational evidence that species have not fundamentally changed over the last 4000 years in my next post.

Noah’s ark results in a massive loss of genetic information. Ken Ham likes to say that all species are losing information over time but he never mentions the single greatest event of massive information loss in earth’s history.  He would find that evolutionists would completely agree with him that if all animals were restricted to a bottleneck only 4500 years ago then that would truly represent a serious loss of information during that time.  But as I just indicated, Ken Ham can’t afford such a massive loss of information at this time. He desperately needs exactly the opposite.  He needs that bottlenecked pair to have the most variation of any pair of animals in the history of the world for his hyper-evolution by natural selection to have any hope of working.

Look at it from the perspective of a gene (more on this in a future post).  If there were 200 different forms of a particular gene in the members of a “kind” before the flood how many of those variants could there have been on the Ark? Not many.  Each parent could have had two versions at most because animals all have just two copies of their genes.  Add to this the problem that genetic sorting had been going on for 2000 years before the flood and so no two individuals are going to have anywhere close to a high percentage of the original created variation.

How can YECs rescue themselves from this population genetics nightmare?  I really don’t know because I have found hardly a mention of this problem in the YEC literature.   But there is one hand-wavy explanation that I have been given when I pose this question in person.  It has been suggested that there was a special preservation of genetic variation by God in the two animals he brought to the ark.   God performed some sort of supernatural direction of a male and female that represented the two most extreme genetic versions of the “kind” being directed to come to the ark thus preserving some – but still only a small fraction – of the original variation of the “kind” on the ark.

This solution is no solution as you will see in my next post where we will look at some specific examples but for now I want to point out a very practical way that AiG has not thought this through and seems unaware of how profoundly problematic their hyper-evolution hypothesis is. And that is all that it is, a hypothesis.

Answers in Genesis is producing animals for their Ark Encounter that supposedly demonstrate what those common ancestor of today’s species may have looked like in Noah’s day.  And what did they look like?  They looked like a mixture of today’s species but they also are portraying the male and female as very similar to each other as if they are the same species. But if God directed the most genetically diverse pair of animals onto the ark the males and females of every kind should look as different from one another as possible rather than the same as they are being portrayed.  For example, I would advise them to be showing a male lion and female leopard boarding the Ark rather than two lions as seen in all their advertising.  This would seem weird to most of their target audience but they claim to be representing the best creation science has to offer on this ark.

Genetic bottlenecks are a serious challenge to all species when they occur. The negative effects of bottlenecking are well documented and profoundly effect the fate of species.* YECs are faced with a serious problem that challenges one of the most fundamental concepts that Ham’s post-flood evolutionary ideas depends upon:  the presence of fantastic amounts of genetic variation in the progenitor to all current species.   No amount of crossing over or hybridization can create new genetic variation/combinations where no variation already exists.   The only thing a population that has bottlenecked can do is wait for mutations to add new variation to a population allowing the processes of natural selection and genetic drift to once again begin to act.   Unfortunately for the YEC, mutations are not that common nor do most creationists want to invoke mutations as a source of genetic variation that natural selection can use to adapt a species to its environment because that sounds a lot like adding new information to a species and that would really sound like they are embracing evolution.

————————————————–

Below is a figure from another article I wrote on this topic:  Are ruminants derived from a common ancestor?

A representation of a possible young-earth hypothesis for the origin of the members of the Order Ruminatia. Other ruminants are not considered related to those in this group. Figure: Joel Duff, images from Wikipedia (see attributions at the end of the article).

A representation of a possible young-earth hypothesis for the origin of the members of the Order Ruminatia. Other ruminants are not considered related to those in this group. Figure: Joel Duff, images from Wikipedia (see attributions at the end of the article). Notice the massive bottleneck. Where did all the variation come from to make all these ruminants?  That is a lot of evolution and yet to resources (variation) for evolution to use.

* It isn’t always the case that species that are reduced to small numbers are sickly or not otherwise adapted to their environment. The remaining individuals may have few deleterious alleles and may, in fact, have lost some bad alleles that were in the larger population. But the bigger problem is that with reduced variation there is little for future populations to work with if the environment changes. In this way the long term viability of a species is in doubt.  Some may do fine as they are for long periods of time. Cheetahs and walruses seem to be doing just fine but more species will go extinct under such conditions than will survive in the long run.

Comments

  1. Nice take-down.

    Like

  2. wowfunny251 says:

    Not that I agree with Ken-Ham. But I think the idea is that post-flood mutations only deleted information in the genome, not adding new information. Though given how some species have incompatible information…

    Liked by 2 people

  3. christopher kederich says:

    Unfortunately, the sort of people who put forth and propagate the YEC theories are not only non-scientists, they are typically anti-scientists, who find no problem in using all the benefits of modern science (fuel, transportation,communications, medicines, cosmetics, etc.). They seem to see no hubris in making up fantasies to fit their whims. It is rather like another fiction you may recall, in which the binding energy that holds together the universe turns out to come from bacteria in the blood that also allows its users to jump around and duel one another like performers in an Oriental action movie. Star Wars, in case you don’t know.
    This is not lack of information or understanding, but a rejection of it. It is a problem of the spiritual heart, and probably needs to be addressed as such.

    Like

  4. Excellent article. I recall reading about a species of hawk or falcon that had been reduced to a single breeding pair, but there was enough genetic diversity in them that the resulting descendant population is doing well without genetic diseases and is no longer considered critically endangered, although There is probably strong genetic evidence of the recent bottleneck (I think it was in the 70’s).
    As I recall (quite possibly incorrectly) it was in Jerry Coyne’s ‘Why Evolution Is True’.

    Like

    • Excellent information. Just a question: Is it simply an issue of insufficient time between the ark and today that is the issue or are there others? I know there is a second article coming. I ask this because even belief in a single common ancestor faces a bottle-neck issue of sorts, doesn’t it? Given enough time will cheetah’s diversify (if they survive their current genetic issues)?

      Like

      • datadroid says:

        Generally, as pointed out in the article, a diploid organism will have at most two copies of a particular gene, for a total of four for a breeding pair. If each of those represents a different allele (gene variation), you can have four different variants within that population. Mutations (copying errors) are rare (1 in 1-10 million or so per generation, depending on the type of organism and environmental factors) so by observing the genetic diversity of an extant population, a reasonable estimate can be made of its lowest population level as well as how long ago that level was reached.

        The evidence from all relevant fields of study, particularly genetics, overwhelmingly supports the idea that all extant life is descended from a universal common ancestor living almost 4 billion years ago–more than enough time to reach the observed level of genetic diversity. Cheetahs are mentioned in this article as they are a well-known example of a severe genetic bottleneck (possibly fewer than 7 individuals around 10,000 years ago: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC46261/ https://prezi.com/vbg5rbufbk44/evolution-presentation-population-bottleneck-and-cheetahs/). However, you’ll note that even this is more than two individuals and longer ago than 4350 years ago.

        If all extant species were descended from a single breeding pair, they would all be even more genetically restricted than cheetahs are today.

        Liked by 2 people

      • Excellent questions (Megasolipsis and Ron). I added a short note to the bottom of the article to clarify a bit. When a population is bottlenecked the surviving individuals may be just fine in term of their health/fitness. They will have some variation as all members of any species does. But that variation can only be a small subset of what previously existed. As such the species is left with a much smaller gene pool to work with. That might be fine. Cheetahs’ seem to be doing just fine but they are virtually the same in look, behavior and physiology as they were when they survived the bottleneck. Other species of cats which have more genetic variation are able to change over time as a result of genetic drift and natural selection but cheetahs have very little wiggle room. Someday that might be very bad for them but if they can survive long enough they are increasing their genetic variation every generation. Mutations happen (eg. about 50 new mutations occur in every person born and I would think that Cheetahs are probably similar) and so genetic variation is building back up. As variation is built and crossing over/sexual reproduction occur the population will have a greater ability to adapt and survival of the species become more likely. So yes, the simply answer is that it is about time. Mutations that are neutral and position don’t happen at a high enough rate to account for the YEC speed of diversification. If the mutation rate were very high in the past it would hurt the organisms. That is called mutation load and it cant’ go to high. The low rate of mutations accumulation is what is needed over time.

        Liked by 1 person

      • datadroid says:

        Just to clarify, the figure of 1 in 1-10 million refers to copying errors per base pair, not per gene.

        Like

    • wescotdowns says:

      You just rendered his article mute as you pointed out that even small populations have enough diversity to survive.

      Like

      • Only sometimes, and it would leave strong genetic evidence of it happening. We don’t find each species/genus/family having evidence of a bottleneck in the last few thousand years.

        Like

      • that’s funny

        Like

        • There is a deep literature on population size and diversity. We are talking relative diversity here so its important to know just what is being compared. Foxes on the Channel islands have almost 0 genetic diversity even at loci that mutate very quickly. But Red Foxes as a species have very very high diversity even in small populations. But that high diversity is frequently due to high gene flow. Also, small populations have mechanisms to maintain quite a bit of diversity but you have to unpack what that diversity is to find out it is useful or not. I guess I’m saying its pretty complex, no one can just say, there is lots of diversity and so many species could be formed quickly.

          Like

          • I wasn’t doubting your point. I was commenting on the response to the post “you’ve rendered the whole point moot”. Not sure that was poster’s intent.

            Like

          • Wait a second, “its pretty complex, no one can just say, there is lots of diversity and so many species could be formed quickly”? By that logic, shouldn’t you be similarly restrained from saying “there’s no diversity, so species can’t be formed quickly”? The lack of knowledge cuts both ways.

            Moreover, your claim has been that there is very little diversity, so rapid speciation isn’t possible. The way to address that claim is to demonstrate either that there IS tremendous variation or that a mechanism exists by which there COULD HAVE BEEN tremendous variation. I think I’ve made a case for the later based on recent research, whether anyone acknowledges that here or not.

            But you raise an issue that should be central to the continuing dialogue. That is that we don’t actually know what genetic variations were required to bring about the speciation event, and therefore none of us can say whether there was enough variation present or not. You can make the argument that bottlenecks reduced the likelihood of sufficient variation, and I can make the argument that lots of variation is possible; but neither of us knows exactly which variants or how many would have been required. The conversation needs to focus on those questions.

            Speaking to that issue is an interesting new paper that came out in Nature Communications in May of this year http://www.nature.com/ncomms/2016/160517/ncomms11519/full/ncomms11519.html. They sequenced the genomes of giraffe and okapi and compared them to identify putative genes involved in the divergence of the two species from the hypothesized common ancestor. They conclude that the structural and cardiovascular traits that distinguish the two species could be explained by changes in a small number of genes. From my reading of this paper, I would consider this to be evidence (although not conclusive evidence, of course) that the speciation events that created the giraffe/okapi kind would not require as much variation as Joel seems to be suggesting. What is important to note is that there is no mention of novel pathways or even novel genes in the giraffe compared to the okapi, demonstrating that dramatic change within kinds can happen with little genetic variation and no genetic innovation. Thus less time and less variation would be required for the speciation event than conventional wisdom would suggest.

            Like

            • Hi Trevor, that paper leaves out quite a bit about the genomes that I assume will find its way into other pubs but you can see that there are 150 fewer genes predicted in the Okapi vs the Giraffe so either some were lost, some novel or some combination. But I would just suggest that you think about the similarities of the Giraffe and Okapi with chimps and humans in minds. 19.4% of the okapi and giraffe genes make the identical protein. that sounds impressive but about 30% of genes in humans and chimps make the identical protein. They don’t provide total SNP numbers in this papers but I would be shocked if the okapi and giraffe aren’t more different by any genetic measure than humans and chimps. Directional selection of a small set of genes is common between any species pair or even between families. The more important question is how much difference there is at neutral or near-neutral site in the genome since environment/adaption won’t explain those differences.

              Like

          • Your suggestion to interpret the data within the human/chimp context is valid in some cases, but in this situation I’m highlighting the identification of genetic differences that might explain specific phenotypic variation specifically between giraffe and okapi. I’m not really referencing total genome similarity which one could contextualize easier.

            As to the discrepancy of about 150 genes between the two species (162 to be exact), I would hesitate to conclude anything about that number given that gene prediction error rates, depending on the algorithm, can range from 1-15% or more. This paper’s reported discrepancy is less than 1%, thus even the best algorithms couldn’t provide statistical evidence to suggest that any genes were lost or derived.

            I do take your point that many details about the genomes are not described; certainly there should be many more analyses coming from their sequencing projects in the next few years. But let’s consider what evidence was given in the paper instead of what wasn’t. This paper was addressing the genetic basis underlying the emergence of unique characteristics of the giraffe, specifically focusing on the neck and cardiovascular system. Their gene ontology analysis pulled out genetic pathways that could specifically address those characteristics, and half of the 70 genes that showed signs of adaptation were involved in developmental patterning and differentiation. Furthermore, some of those genes were transcription factors that could conceivably regulate somite size, the anatomical feature that, in part, determines neck length. Thus, in the author’s words, my take-home message was that the “giraffe’s stature and cardiovascular adaptations evolved in parallel through changes in a small number of genes.” (emphasis on the small number of genes rather than the notion of evolution. Just an aside). The broader conclusion is that the dramatic changes between species that lead some to require massive amounts of variation and time, could potentially be explained by changes in only a small number of genes, and by extension, perhaps a shorter period of time that could fit the flood model.

            Like

  5. Onlycurious says:

    What would you say to those who claim that preflood animals brought on the ark had every single variation combined in a “super genome”?

    Like

    • Yes, that is a good questions because I have heard this proposed. First, YECs should be ready to call that a miracle. That might sound strange but I have found that YECs will go to extremes to avoid invoking miracles except when they absolutely have to or the Bible just makes it clear it was a miracle (like the closing of the door of the ark). Also, they have to recognize how miraculous this is, it is not just a matter of bringing the right two individuals to the ark to be preserved. Any individuals will have a small subset of the variation of a species so God would have had to supernaturally created new genomes for these organisms or infused new changes in them to pack them full of variation. Second, all that said, it still isn’t’ possible as hopefully I will be able to show in the next post. An individual only has two copies of a gene and so they can’t have hundreds of different forms of that gene but only 2 of them. It is a bit more complicated than that but the totality of the variation that we see today in any species cannot be contained in two individuals. YECS will have to postulate that the original genomes of these animals were larger and had more copies of genes and then somehow degraded to lose half their genomes over time. We see no evidence of this happening. Even in the case of humans, which YECs haven’t diverged into hundreds of species like other species preserved on the ark. No two people could have all the different versions of the genes that exist in the human population today. So where did that variation come from? Does that mean there could’t have been two people originally one might ask. That variation comes from new mutations which include those created with chromosomes interchange material. Mutations create new alleles (version of genes) in the population. So the original common ancestor doesn’t need to contain all that variation. IN other words,no “super genome” is required. Now YECs will admit that mutations happen but they want to limit their importance and so any mutation that could create a new character such as wing size, color, beak shape etc. isn’t one they want to say came into existene and they would rather say those verions of the genes were in the original ancestor. But there just isn’t any room for them there. So mutations must be the answer to where variation comes from but YEC can’t go down that road because it will quickly lead them to evolution of new characters which they say is impossible.

      Liked by 2 people

      • Onlycurious says:

        Thanks for your resposne.

        I don’t know much about DNA but I don’t see how any organism can have so many variants packed into its DNA. I don’t think such an organism would be able to live, and all of them should be activated, so I don’t see how ones could be selectively deleted if they’re all activated at once.

        The DNA would be so different I doubt it could even be considered DNA at that point.

        Does that sound about right?

        Like

      • “Now YECs will admit that mutations happen but they want to limit their importance and so any mutation that could create a new character such as wing size, color, beak shape etc. isn’t one they want to say came into existene and they would rather say those verions of the genes were in the original ancestor.”

        We YECs have no problem accepting mutations or variations that alter “wing size, color, beak shape etc.” We *do* take issue with the notion that mutations will create a wing or a beak de novo. These are two separate issues. Thus we accept, acknowledge and appreciate mutations, but we stipulate they we don’t believe they create variation outside the barrier of a kind.

        Like

        • Quick thought: but any new variation that didn’t exist in the original kind is a variation that is outside of the original kind. How then will a kind remain a kind if it is allowed to change? Sounds trivial but you have made one big step down a slipperly slope once you allow any new variation that God didn’t originally create. A different color might sound like nothing but when it is combined with 200 other trivial characters you suddenly have a lot of change and a thing that you might not think is the same as the original kind.

          Like

          • wescotdowns says:

            Every feature preexisted because that is the way dominant and recessive work. They have also found that many genes work together even if their primary function may be like color of hair. The diversity is in the complexity of the created being.

            Like

          • Wescotsdowns, regarding dominant and recessive: The don’t believe that a majority of alleles come in dominant recessive forms but are more likely co-dominant or incompletely dominant. All those alleles for metabolic enzymes make make many different versions of the enzyme each of which has different activity but none of which are dominant over others. Really, recessives are usually broken versions of genes which doesn’t sound like something that would be in the originally created kinds. Recessives are frequently if not usually alleles that have mutations that kill the function of the allele thus making the other working allele the dominant one because it is the only functional one. YEC models don’t ever talk about this but rather use dominant recessive because they know that most people will only remember mendelian genetics from high school in which he discovered dominant recessive traits. But as you say genes work together to form combined effects or are additive affects. These aspects of genetics are far more problematic to the YEC model than dominants/recessives.

            Like

  6. Joel, you’ve made some strong assertions here that I feel are not well balanced or at least need to be vetted. Particularly you’ve hung your hat on two statements that I find dubious. The first statement is “[…] species that have been reduced to small population sizes lose their genetic variation become essentially clones of one another.” Also, you stated that “Noah’s ark is the ultimate population, and even species, bottleneck which would have eliminated the vast majority of genetic diversity in all kinds.” My initial impression of these statements is that you’ve traded careful nuance for hyperbole. But based on the decided tone of your statements, I assume you have a body of literature on which to make these statements?? Could you enlighten me? Meanwhile, I’ll try below to explain where I feel your assessments have gone wrong.

    First, a bottleneck could cause the loss of some or even many genetic variants, but it’s hardly absolute or all encompassing as suggested in the quotes I gave above. Research shows that repeated bottlenecks, especially in the context of domestic plants and livestock, yield the highest losses of variation; this of course does not pertain to the Ark event as it was a single bottleneck of wild animals. Moreover, although the ark bottleneck was extreme, Miller and Hendrick (J. Evol. Biol. 14[2001]595-601) suggest that it’s not the magnitude of the bottleneck that results in the loss so much as the pattern of recovery afterwards. This of course highlights that recovery of variation after a bottleneck is a reality, but you don’t mention that anywhere in your post. This is sadly misleading especially in conjunction with other statements like “these populations cannot evolve by natural selection or genetic drift and thus will not change over time.” This statement is simply not true (the fate of the cheetah is hardly the rule). Bottlenecks are most harsh towards rare variants but keep the sequence diversity largely intact (here’s one example: Proc Natl Acad Sci U S A. 2006 Nov 7; 103(45): 16666–16671). So I take issue with phrases like “vast majority,” “all kinds,” “become essentially clones” and “will not change over time,” as these phrases do not accurately represent the genetic realities of bottlenecks.

    There is a massive amount of genetic variation in animals today (and there could have been even more during the time of the ark considering what we know about loss of variation). In point of fact, creating statistical models to derive meaning from all of the assayable variation is a very real hurdle in genomics today. So the loss of some of this variation may not have created the genetic catastrophe that you are painting here. In short, the diversity may have been pared down from gargantuan to just huge while remaining sufficient to create the striking phenotypic diversity among the kinds we observe today.

    Because of the imbalance of your bottleneck description, you’ve created a false dichotomy in which you state one conclusion as the only possibility while ignoring other legitimate options. For example, bottlenecking after the ark doesn’t necessarily preclude Ken Ham’s model. It’s a perfectly reasonable conclusion that the genetic diversity that we see today is simply the remainder of the pre-flood diversity minus that lost in the ark bottleneck, and that there was sufficient variation at the time of the ark bottleneck to produce the variation in question (and I don’t even need to postulate divine maintenance of genetic variation). Exaggerating the mechanism behind bottlenecks in order to cast doubt on Ham’s ark hypothesis is not our only interpretive option here. In fact, I think that you are painting an unnecessarily bleak picture of bottlenecks. Certainly they do reduce diversity and could thus stifle future adaptation, but it has also been demonstrated that bottlenecks can be the very stimulus that *leads* to new genetic diversity of an additive nature, and even brings about new speciation events (see Miller and Hendrick’s introduction for comments and further citations). Essentially, your bias against Ken Ham has caused you to miss a important aspects of genetics that may actually *support* the YEC position. Specifically, Miller and Hendrick suggest that bottlenecking could very well lead to additive genetic variance, at the same time reducing fitness in the population; this paints a picture that bears strong resemblance to what the Bible reports and Ken Ham is suggesting; i.e. a huge bottleneck which resulted in additive variation, speciation events within kinds and reduced fitness indicated by shorter life spans.

    One final note; I want to point out that your examples using cheetahs and Dalmatians are not relevant to the ark context, since both of those species represent genetic “dead ends,” if you will, that resulted from repeated, natural and intentional bottlenecks. While they represent the potential consequences of bottlenecks, they do not accurately represent the animals that came off of the ark which would have had a full complement of genetic variation. So a Dalmatian’s inability to diversify beyond its current state does not in any way preclude such diversification in the animals exiting the ark.

    Like

    • Hi Trevor, all bottlenecks will have somewhat different results depending on which individuals survive but even if it were possible, which I will just say it is not, for some pair to still have enough variation to sort out into a 50 new species, one could not expect hundreds of simultaneous independent bottlenecks (which is what Noah’s ark represents) to all end up being the most favorable least damaging possible bottlenecks. Surely many would have experienced the worst effects and had no ability to speciate afterward. Even the most optimistic scenarios of aftereffects of bottlenecks don’t look so good for the YEC needs. Also, the extremes of the ark can’t be overstated. A bottleneck of 10 individuales I would think would have an order of magnitude more variation preserved than a 2 individuals. Most research and models are concerned with bottlencks bringing populations down to the hundreds of thousands not to 2. So when even those scenarios leave the species with reduced variation one could only expect the ark scenario to be much worse.
      I think you have to consider that just saying there was a lot of pre-flood diversity isn’t enough. That diversity would have been parsed into many small pools of diversity in species and then even smaller pools of genetic diversity in individuals by the time of the Flood. Without invoking supernatural insertion of new variation into the ark survivors they couldn’t hold but a fraction of the original diversity.
      Small populations sizes after the flood although they would aid the power of genetic drift also would cause higher rates of loss of genetic diversity. I agree that genetic bottlenecks often lead to many new opportunities and evolution of new species but not in the short run. All of the native species on Hawaii started as a very small number of founders and they evolved into new species, genera and families but it takes a lot of time for the requisite mutations to occur to allow for all that new speciation. The honeycreepers are all evolved from a single common ancestor for example but it is thought this has taken several million years. But they are very successful even as an extremely bottlenecked group originally.
      Yes, Dalmatians are dead end because of artificial selection. They can not be changed into any other dogs. But I guess that is the point, all the ark animals are similar dead ends. Even if they had 10x the genetic potential they would still be quite limited. Put it this way, without needing to have massive evolution after the ark, would any YEC predict that 2 animals should be able to diversify into hundreds of species? What reason would they have to expect or predict this behavior? There is no biblical reason, since the exception is that the animals people see will not change their spots (of course in the YEC model, ironically the leopard didn’t exist and so did change its spots – I know the context is the individual not the species over time but the idea is there that animals aren’t observed to change).

      Liked by 3 people

      • Joel, your ideas of variation are not current with new advances and knowledge. The notion that all of the variants that effect a gene reside within a 1970’s definition of exons and introns and two alleles is out of date. There are other pools of variation that we now appreciate; in addition to the two copies of each gene traditionally thought of as alleles, we know appreciate the role of intergenic variations that offer discontinuous grades of heritable variation which can be shuffled by crossing over to create staggering variation. Going further, single cell DNA sequencing in the last 4 years (Cell. 2012 Jul 20; 150(2): 402–412) demonstrates how this variation is represented intact across hundreds of millions of astonishingly heterogeneous sperm from a single donor (this variation was previously masked by genetic analyses of sperm populations rather than single cells). So when two animals create offspring, they have the ability to pull from a tremendous amount of allelic variation far beyond that suggested from intro biology classes. When the animals left the ark, they left with a massive amount of variation that could be passed to subsequent generations. This isn’t just an empty statement, but you’ll have to read the literature to appreciate it. Even if the variation was parsed out into 50 or even 500 offspring, its becoming obvious that there was plenty to go around. To answer your question earlier in the post about where all of this genetic variation comes from, Wang et. al. 2012 suggest that it comes, at least in part, from variable recombination hot spots which create an incredibly variable sperm population with subsequent variation added in new generations. You don’t see this variation in a single sperm/egg combination, but you see it in the sperm population of a single individual. So in reality they don’t have just 10x the genetic potential (as if you were being generous), they have almost infinite genetic potential; even in a single animal all of the genetic variation you are asking for exist in a single individual and there is no need to postulate divine intervention. It is no longer defensible to suggest that the animals on the ark could not have given rise to the variation we see today.

        Like

      • Hi Trever,

        (I couldn’t see a reply button to your last post, so this is being linked to the one preceding it). Can you clarify some of this? You seem to be discussing nothing more than meiotic recombination, which has been known since the 1960s, and although there seems to be some evidence that this can sometimes lead to the formation of new alleles, since recombination does not respect reading frame boundaries, we don’t seem to have much evidence for this often being the way in which new alleles are formed. You go on to say; “we know appreciate the role of intergenic variations that offer discontinuous grades of heritable variation which can be shuffled by crossing over to create staggering variation “. Aren’t you just pointing to the potential variability intrinsic in polygenic traits here? I’m sort of guessing at your meaning, since it is not entirely clear to me (probably other readers have a better idea of what you have in mind) and there are no references, but what you are calling “pools of variation” seem to be nothing more exotic than this. Is this right or have I misunderstood your allusion?

        Wang et al. 2012 points out the well known reality that “meiotic recombination shuffles the two haploid somatic genomes to create a unique hybrid haploid genome for each gamete cell.” While true, he’s not saying anything other than the fact that genetic crossover between parents will lead to a unique overall sequence in each chromosome, and each coding region will still simply be made up of some paired combination of the parental alleles. It is not at all clear that you can take a given polygenic trait, and with just the right shuffling of the available genetic material (based on a very limited set of possible alleles after a genetic bottleneck), end up with the immense diversity of often extreme features found in the many daughter species a few hundred years later. Such a claim would need a great deal more evidence than it has and the position seems to gain no support from the rates of genetic change and speciation seen today, especially after genetic bottlenecks.

        And forget the phenotype for a minute; can’t we just test whether this is reasonable by way of a comparison of the great genetic diversity in any coding region within each created kind? If you take the genetic diversity for each region between all of the daughter species (and within each of those species), and compare it to maximum rate of change that can be supported in terms of mutational load (or more reasonably, with the rate of change observed for any species undergoing adaptive radiation), using the limited timeframe allowed, I think you may have a pretty good test for whether such a scenario is even remotely possible, let alone whether it actually happened this way.

        One way or another, the bottleneck seems to remove nearly all of the diversity for each allele, so any measurement of future diversity at this same allele can give an impression of whether or not a certain rate of change combined with a certain amount of time can result in this outcome. Do you agree with this or did you have something else in mind when you mentioned pools of variation? If you did have something different in mind, can you point me to some references so that I can see if you have a plausible case for how great diversity can quickly arise after an extreme bottleneck?

        I apologize if the answers to some of these questions are trivial, but I simply can’t see how your proposal works at this point. I’m not really looking to step into a debate here and I am not sure I am equipped to do so, I just want references that can allow me to verify, to my satisfaction, whether there is some element I am not seeing that can contribute to a defense of the creationist position, since I think the above blog makes a fairly solid case against it.

        Thanks

        Liked by 1 person

      • Hi Approved Money Changers,

        I’m not pointing to polygenic traits. These are not traits being regulated by multiple genes. They are traits being regulated by genes with newly appreciated, expanded boundaries. I’m referring to the idea that the definition of a gene is changing. We no longer think of a gene as a well delineated sequence of nucleotides downstream of a few kilobases of promoter sequence. We understand that the 3-D conformation of the DNA brings traditional gene bodies into proximity with sequences otherwise megabases away. We are starting to understand this 3-D conformation as part of a gene. So to say that all of the variability of a gene resides within a few exons and introns is not the current understanding. Allelic variation is now far more tramendous simply because the definition of a gene has expanded. Crossing over therefore shuffles a much larger region which can be segregated in more ways given that there is now more distance between regulatory regions for recombination to happen.

        With that being said, the problem with the notion of variation that is being put forth on this blog is the assumption that the only variation available to be propagated is what was passed on in the chromosomes derived from the parents. In reality, when those parental complements of chromsomes are segregated and expanded into a population of sperm, each of those meiotic events is now underderstood to be incredibly unique due to varible recombination hot spots and randomly aquired mutations. The result is a population of hundreds of millions of unique sperm that contain enormous variation. So its not simply an issue of meiotic recombination, its a new appreciation for the fact that each meiotic event creating every sperm is incredibly different. We didn’t appreciate this before single cell sequencing because much of the variation was diluted by analyzing populations of cells.

        Its now clear that If you looked at the inheritence pattern of a single variant (maybe a SNP or a mutation) in all of the progeny of an animal just off the ark, you may very well have seen a mendelian pattern; but when you look at *all* of the variation across the entire genome, you will find that every progeny is tramendously variable (essentially a unique genome), and that variation, I believe, could easily provide the diversity among kinds that we see today. If you talk to the cytogeneticists in my department, they will tell you that every disease causing variant known in the human population is represented in a single individual’s sperm population at any given time. Look back at the Wang paper at figure 5 and you’ll see differences between individual sperm cells that include missing entire chromosomes in some or even whole-chromosome aneuploidy in others. So in this one analysis of 91 sperm you see “normal” cells in the same pool as cells that harboring large deletions that could lead to devestating skeletal absormalities. This sort of genomic specturm is the true picture of genetic variability.

        Like

      • Hi Trevor,

        Thanks for your clarification. Yes I certainly agree that the picture is more complex and multidimensional than once thought. With cis- and trans-acting elements in play and the shuffling of multiple interacting blocks through recombination, we can no longer look at the genome in simplistic terms. That said, it is not at all clear that the genetic sorting of the kind that you refer to translates into significant phenotypic differences of the kind that we see between species. This is certainly not established by the paper you cite. The higher level genetic interactions you refer to generally have to do with gene regulation more than anything else, so while this might result in some developmental difference, I can’t see how this allows us to move between species in the manner that it would need to. Even if such effects were possible, which has yet to be established: if routine recombination allowed such transformations to occur, we should see essentially no species-level fixity, and if such shuffling alone could result in the tremendous differences seen within, for example, the ruminant kind, then this sort of dramatic variation should be seen today.

        The observation that there are recombination hotspots and that it isn’t only large blocks that are exchanged does not do much to change this picture; the assertion that this can result in phenotypic changes to this extent remains nothing more than a suggestion, one that is ostensibly falsified by the actual outcome of recombination today.

        You then go on to infer, in another post (and this is presumably a way to account for the fact that we don’t see these effects today), that we may be reaching a completion of the spectrum in terms of the range of viable variation, but this doesn’t make sense to me for a few reasons. If this type of recombination of the genes found in two individuals can lead to such a massive amount of change in their progeny, with mutation playing a negligible role, then unless we are seeing frequent and sudden reversions to any other species within the kind (as old combinations or already extant combinations are hit upon, since new combinations are of limited availability ex hypothesi), there must continue to be an enormous amount of untried potential based on recombination alone. In which case, we would see normal recombination resulting in continued rapid speciation (since a slowdown in speciation implies an exhausting of the potential diversification in your view). You also mention and exhausted range of “viable variation”; which would mean that wherever we do not see one species giving birth to the same or to another species within the kind, any new combination would result in death. And again, why would we expect any species stability at all, if the genetic potential intrinsic to the kind is still available for each reproductive event based on recombination alone; after all, the past recombination events do not tend to involve any loss in genetic potential?

        In order to account for the far lower speciation rate, you need a massive loss of genetic potential over the last few thousand years (such that we don’t see the results that would be needed to confirm this original massive radiation of species). Your proposal does not include this loss of potential; if the same kind of recombination leads to such diversity in the haploid gametes of one individual and once led to enormous phenotypic changes, then why doesn’t this huge variability ever translate into the significant phenotypic changes required for rapid speciation today (i.e. any of the viable sperm cells tends to give rise to something rather similar to the parents)? The haploid genomes of the individual all show a unique reshuffling, yet we have no indication at all that this results in the kind of end-point variation that you require. I assume you would like to look at mutations as the source of this loss in genetic potential, but it is difficult to see how the argument is supposed to work. I would appreciate if you would explain how mutations or anything else results in exhausting the potential that recombination is supposed to tap into, since your proposal seems to be completely independent of mutations.

        Further, we are in a position to test this timeline fairly directly, as I mentioned, based on the degree of change observed within limited regions in the genome due to mutations. Taking a non-coding region where there is little reason to assume to assume a critical function (it should be an even lower rate of change if there is an unknown function), does the rate of change between species within a kind match the upper mutation limits applied over a few thousand years?

        You have pointed out only that recombination results in many unique genomes, but I don’t think that this really plays out as a working hypothesis unless these issues are dealt with, at least for the time being. I’m sorry for the extent of the above critique, and some if it might certainly be based on my own misunderstandings of what is being proposed, but I don’t see this working as a hypothesis, and I think it only really works to buffer the position against the problem that this bottleneck represents.

        Thanks,

        Liked by 2 people

      • Thanks again Approved Money Changers,

        No need to apologize for a long critique since my critique was pretty long as well. I think you make some good clarifications here. Here are a few of my thoughts.

        it is not at all clear that the genetic sorting of the kind that you refer to translates into significant phenotypic differences of the kind that we see between species. This is certainly not established by the paper you cite.

        I agree. It is not clear, and I don’t claim that it is. I’m using the Wang paper to demonstrate that, although Joel is trying to make it seem as thought there is very little variation available, there is actually a tremendous amount of variation. Not knowing if that variation is function doesn’t diminish the fact that is exists and could very well be functional. And again, the Wang paper is not simply showing recombination and sorting. Its showing new variants. There are additional chromosomes (and losses) and de novo mutations as well. I don’t claim to know that those variations are meaningful, but as a geneticists, my experience and education tells me they often are. Most importantly, the fact that we don’t know is as much of a problem for your argument as it is mine.

        if routine recombination allowed such transformations to occur, we should see essentially no species-level fixity, and if such shuffling alone could result in the tremendous differences seen within, for example, the ruminant kind, then this sort of dramatic variation should be seen today.”

        Again, this isn’t simple shuffling. New variants are coming onto the scene. But moving on, I think the species level fixity happens even in the face of this new variation because random variation cannot create new biological innovations, but it certainly can and does modify existing ones. I’ve argued in previous posts that the grouping of kinds seems to place species together that don’t have radically new innovations, but rather variations of those that exist; longer necks and legs, differently shaped noses, or perhaps the complete loss of a trait like antlers, for example. None of these changes requires new information on the order of genes or networks, simply a modest change in the information that exits.

        the assertion that this can result in phenotypic changes to this extent remains nothing more than a suggestion, one that is ostensibly falsified by the actual outcome of recombination today.

        Perhaps rather than a suggestion I would call it a hypothesis, one for which I have preliminary data. And I don’t accept that it has been falsified by today’s recombination outcomes, because today’s genetic environments are conceivably very different that they were at the time of the ark. There is a logical fallacy that is commonly committed in the larger YEC/OEC debate that must be brought to light here. It happens when an OEC proponent takes a YEC argument out of the YEC construct, places it in the their OEC construct and then destroys it. This often happens (probably unintentionally) because OEC proponents accept uniformitarian constructs but YECs don’t. So OECs want YEC arguments about the past to be testable today, but this simply isn’t always possible. I believe we have one such instance here. You’ve taken my argument about genetic diversity out of its ark-time context (where genetic diversity may have been greater due to fewer historical bottlenecks, and the kinetics of genetic change may have differed), and you placed it into your modern construct and destroyed it by demonstrating that it doesn’t hold up to experimentation today. My argument is based on a theoretic, ark-time genetic environment. You can’t take it out of that construct and place it into a modern one. I would love to be able to test everything that I say, but sometimes we simply can’t recreate the appropriate conditions necessary for contextually sensitive experimentation. In this case, we simply can’t go back to the exact genetic environment that existed in the animals that got off the ark, but that doesn’t change the fact that the differences could be real and could drastically effect our understanding of genetic variation. This is why I’ve pointed out many times on this post that cheetahs and dalmatians should not be used as argument here.

        In order to account for the far lower speciation rate, you need a massive loss of genetic potential over the last few thousand years (such that we don’t see the results that would be needed to confirm this original massive radiation of species). Your proposal does not include this loss of potential; if the same kind of recombination leads to such diversity in the haploid gametes of one individual and once led to enormous phenotypic changes, then why doesn’t this huge variability ever translate into the significant phenotypic changes required for rapid speciation today

        Yes, this is something that I’ve considered. A loss of genetic potential is only one possible explanation. But I think the actual reason that we don’t see the speciation rate today is because we have begun to reach the limits of variable space within the created kind. This is not to say that new variation won’t arise, but rather that so much variation has already happened that there are fewer variations whose phenotypes we haven’t seen; so its taking longer and longer to see them emerge. Its an issue of probability, potential. Consequently, my ideas don’t include mutations as an explanation.

        Further, we are in a position to test this timeline fairly directly, as I mentioned, based on the degree of change observed within limited regions in the genome due to mutations. Taking a non-coding region where there is little reason to assume to assume a critical function (it should be an even lower rate of change if there is an unknown function), does the rate of change between species within a kind match the upper mutation limits applied over a few thousand years?

        As I described above, it really is hard to test this today simply because, as I believe, the genetic environment would have been very different back in the ark days. I won’t belabor this point here since I discussed it above. More importantly, I have to disagree with anyone in 2014 who assumes a non coding region has no critical function. In the days of the ENCODE project, etc, this is just not a reasonable assumption anymore. We are only finding function in the genome these days, not lack of function. So I disagree with your proposed test on a number of levels.

        Thank you for your well reasoned, sincere critique of my ideas. I take them seriously and appreciate your gracious tone, but in the end I still find that they don’t move me from my understanding of genetic variation as I’ve discussed it above.

        Liked by 1 person

    • Hi Trevor,

      Thanks for a very helpful response. I will not work through every point, but I can say that I think we ultimately approach the issue from very different angles. On one side, you find it a doubtful premise to suppose that there was sufficient consistency between past and present mechanisms to enable us to test hypotheses about the past using current observations. On the other hand, I find it more credible to expect a greater degree of consistency between the genetic environment (or other features of the natural world) a few thousand years ago and today, and I think that any proposed radical transformation of this environment should ideally to be supported by evidence or some falsifiable hypothesis as to what may have produced such a change. I also get the impression that all of the patterns in the available data throughout the sciences support the conclusion that the same mechanisms were at work in the past, and that where they weren’t, the breakdown in these patterns tell the tale (e.g. in spite of any uniformitarian assumptions, we do not conclude that the days were always the same length or that the atmosphere was always aerobic, because the evidence does not seem to support these positions beyond a certain point). I think that the majority of these patterns, genetic and otherwise, become very difficult to explain on the assumption that there were such major shifts in the past. Ultimately, the hypothesis that the relationship between genotype and phenotype was not comparable at that time of the ark serves to protect the past, in effect, from the fact that currently available mechanisms do not support the required degree of rapid change, although it may theoretically be true regardless of this fact. I agree with the nuance that we need to think in a context-sensitive manner, but I ultimately think that this precaution is overstated when in largely bars the past from scrutiny.

      In this sense you deny the validity of extrapolations where I consider that there is little reason not to take them seriously, and it is probably unlikely that we will agree on this.

      On the other hand you assert with some confidence that we can extrapolate functions for all DNA based on the ENCODE project (which somewhat notoriously overstated their conclusions and were not sufficiently wary of false positives according to many observers) and on the fact that we tend to be discovering new functions all the time (this seems to be an artifact of selection bias, since obviously no one is announcing or publishing whenever they find no function for a sequence). This is hardly impossible, but I find such an extrapolation unconvincing, given the number of pseudogenes, repetitive elements, duplications etc, all giving rise to the impression that the genome is as much a workshop as a finished product. I find it interesting that we both treat extrapolations in different ways depending on the context.

      You state: “I think the species level fixity happens even in the face of this new variation because random variation cannot create new biological innovations, but it certainly can and does modify existing ones.”

      I think I addressed this, albeit not very clearly, in the previous post. While this may explain kind-level fixity (although I’ve never been clear on how these proposed boundaries are supposed to remain fixed in the context of mutation, natural selection, drift, exaptation etc.) it does not explain the fixity of species unless each instance of recombination involves a progressive loss of genetic potential (a clear mechanism is needed if this is the case). Without this loss in genetic potential, the whole range exhibited by the kind should theoretically remain available for each new generation. And as I discussed, if all of the possible combinations represented by the genetic potential of the kind have been tried and are represented in the natural world, then we should be seeing species changing to other already extant species within the same kind at the same rate that the initial speciation was occurring after the bottleneck. In other words, new changes within each kind would now usually be a rehash of already explored variability instead of a radiation to untried forms within set limits – this would follow from the statistical considerations you were pointing to. I just think something is missing here in order to explain why we are not seeing these continual reversions within the limits of the created kinds or on the other side, why we are not seeing a continued high rate of speciation.

      I appreciate your clarification that you have no intention of presenting a full blown hypothesis, and that your points were merely intended as a correction/clarification, establishing that variability is not just a function of the number of alleles available in a population. Taken as such, I think you make a legitimate case, although I don’t think it really dispels the problem being presented.

      On a side note, I have to admit that I have too often been entangled in discussions with creationists who seemed evasive, misinformed, and even dishonest, while you have proven to be the opposite on all counts, so it is a pleasure to have a solid counterpoint to any prejudices I may have been working on! This is proving to be a helpful exploration of the issues involved.

      Thanks,

      Liked by 1 person

      • I’m happy that you think this has been a fruitful exchange, and I totally agree. Although this is not a comfortable forum for me as a YEC, it remains a very fruitful environment for me to test my ideas and knowledge, since no one here is going to cut me any slack :). I agree with you that we come at these topics from very different perspectives, and although I don’t expect we will sway each others’ ultimate world view much, we will certainly balance them. That’s the most important thing for Christians in the end, I believe. I’m not here to be proven right. I’m here to find the truth about God and his creation. So thanks to you, Joel and others on this blog that help me do that. Looking forward to more exchanges in the future.

        Best

        Liked by 1 person

  7. Jimmie Montgomery says:

    I’m an OEC of the literary framework explanation school and possibly the time expansion explanation of G. Schroeder. I’m aware of the different interpretations on Genesis. I live in a small town in the mountains of NC and appreciate the geology of the region. I highly recommend the book “The Origin Of Mountains” by Cliff Ollier and Colin Pain. I just don’t know how one could maintain a YEC position if they read it with an open mind. If the flood of Noah deposited all the sediments of just the Grand Staircase then the amount of solids mixed in the water would be about as thick as a mudslide, well maybe a bit less, but not by much and definitely a sea of mud if you count the other fossil bearing sedimentary rock. Lots of “hypercane” activity, I’m surprised any plants especially the delicate ones or small freshwater fish survived. I was a YEC back in the late 70s and 80s.

    I do not know if YECs remember, but the ARK in those days was big enough to hold all the land animals that ever existed. I had the first edition of Henry Morris’ commentary on Genesis. I gave it to a YEC pastor friend of mine as he went over the wall about it because it was autographed by H. Morris himself. The six days of Creation were not well thought out and I do not remember Morris saying anything much about the first verses of chapter two when the creation was reduced down to a day, something about metaphors. Never explained why the metaphor couldn’t be extrapolated to chapter one. The Ark of Noah was gone into with a lot of zeal and explanation, including that it was big enough to hold all the animals that ever lived. They sure have changed their minds a lot over the years haven’t they?.

    It was geology and astronomy that turned me to an Old Earth. I haven’t paid much attention to YECism as it just changes all the time. Not once in the 70s or 80s did I read anything about Ham’s hyper-evolution, it didn’t exist back then. I’m sorry, but it sounds completely ridiculous to me. Even if I were a YEC it would still sound ridiculous. All the cats in the world from a single pair in only 4500 years? All the kangaroos in Australia and nowhere else are their fossils found? All the different ruminants? Are they being honest with themselves? I would have to subscribe to a local flood scenario rather than give any credence to this totally unbelievable rhetoric. I would rather go back to the “we don’t know how big a cubit was” stuff than this unbiblical nonsense and unscientific I might add. You ought to spend some time with a young “ex”Christian who lost his faith over this not to mention some that are trying to make it fit and blocking part of their life from other parts. So much for being one and whole in Christ, huh? I’ve had a YEC show me an article explaining how the oldest tree in the world was only about 2700 years old. Apparently the dendrochronologists well proven and substantiated tree ring dates are as false as careful Carbon 14 dates, which as I remember the YECs used to verify that a piece of wood from Mt. Ararat was in the 4500 year range. They use Carbon 14 dating and tree rings when it suits them and the vilify those that disagree with their hypothesis, if you want to call what they do “hypothesis”.

    I think what hurt the YEC cause the most was the attempt by some YECs in Arkansas to have it taught in public schools. It was a doomed enterprise from the start as it was clearly “science” deduced from the Bible and religion. The secularists started really paying attention to it after that. So Intelligent Design is considered religion as well. I think if ID had come out then it may have been given a chance, but we all know how that is now. Simple math and the volumes of fossils are enough to refute YEC and they still do not even believe the world maybe as old as 10,000 years? Morris said something in his commentary about it. He used to allow for holes in the genealogies of Genesis. All I hear now is 6500 years ago, surely they all don’t subscribe to that view, do they? Ham and his multimillion dollar ministry gets absolutely no credence or sympathy from me. He recieves who know how much in donations a year and he’s using a political trick to stick the taxpayers of Ky to pay for his “museum/park”. I hope he uses some of the money to feed and clothe the poor or to ransom young christians from islamic slave traders. Maybe he does, right? I can’t hear you, I said, “RIGHT?!

    Pardon my attitude as I have been attacked and had people in my church feel it was their job to set me straight. I didn’t go around preaching OEC, but it came out here and there. I’ve been asked to leave a church because of people like that. I do not want to go to a liberal church and I’m not a Roman Catholic so in my little town I do not go to church. I have to drive forty miles to Asheville to worship without being harassed. So, please pardon my poor attitude again. I don’t believe in Dispensationalism or being under the “Law of Tithes And Offerings”. So I get the triple whammy, OEC, no pretrib rapture or even a trib and the worst I did was explain that the church isn’t under the Law and especially tithes.
    Charles Spurgeon is my favorite author and preacher. I believe pretty much like he did too. Get and read the book “Spurgeon And The Hyper Calvinists” by Ian Murray. Quite an eye opener as to what happened to his church after he died and they brought in an American revivalist preacher. One of the first things he did was to try and put the congregation under The Law pertaining to tithing. To tell you about different times and practices, they used to sell seats to people, it wasn’t much, but that’s what they did. I wonder how full our churches would be if a seat in the pew cost $20? Oh, Charles Spurgeon who was called “The Prince Of Preachers”, didn’t think the age of the Earth was a big deal either.

    Liked by 2 people

    • Jimmie, I am sorry you have had such terrible experiences with some Christians, but where in the world did you live? I’ve been a Christian for over 40+ years and have never had a problem sharing my viewpoints about the age of the earth or evolution. I hear of testimonies like yours occasionally and can only wonder where these types of churches are. I don’t doubt that they exist, so don’t get me wrong. I honestly have no idea how old the earth is, and I really don’t care. I don’t accept evolution, but the bible has little to do with it. I just haven’t read anything from the evolution camp that remotely resembles proof, at least reasonable proof. Both sides have lots of theories, and that’s okay, seeing as how neither camp can actually repeat or observe what happened thousands or billions of years ago. Actually, I should have said hypothesis instead of theories. So, sorry for your experience, but don’t give into the temptation to paint with too broad a stroke. I’ve encountered plenty of Christians who don’t agree with me on everything, but it never affected our fellowship. Oh, by the way, Spurgeon was on board with Calvinism, just not “hyper” Calvinism. Don’t let this bitterness interfere with the command to fellowship. Even if you can only do it on line. Wishing you the best. And may I commend those on this site who can disagree to disagree, yet still enjoy the exchange AND learn from it. Kudos to you all.

      Like

      • Chuck, I find it surprising that you haven’t heard convincing evidence for evolution. As someone who has studied evolution, I am constantly amazed by just how much evidence for evolution there is. If you like I can give you some of the more convincing (or at least, what I find more convincing).

        Like

  8. Christine Janis says:

    It makes more sense to me that a giraffe is an act of special creation than to assert that it evolved from a basal ruminant like a mouse deer in a couple of thousand years.

    Liked by 1 person

  9. Hi Trevor,
    However much regulation by all sorts of RNA and retroviruses etc you want to suppose, the unclean animals are just going to have 4 sets of everything. And if you assume that recombination and assortment makes for sufficient differences, then you should suppose we see this type of assortment speciation happen in nature at the moment.

    Liked by 2 people

    • Hi Peter,

      I’ll just make a quick comment here because I answered some of your concern in a response to Approved Money Changers I just posted above. My argument doesn’t suppose retroviruses or transcriptional regulatory mechanisms like non coding RNAs. You can read my comment above for why the simple “4 sets of everything” is too narrow of an understanding. Essentially it doesn’t acknowledge that every single individual sperm cell is a result of a unique recombination even that yields a haploid genome that is notably diverse from its primordial germ cell progenitor (as per the Wang paper we’ve been referencing). So a reproductive individual is not left to simply pass on some combination of their parents pool of variation, but rather they have a huge pool of unique meiotic events that they can pass on. Each of their progeny will receive a genome that, although similar in many ways, is highly variable beyond its parents genomes.

      As to your insistence that I should expect to see this same sort of “assortment speciation” happen today, I don’t deny that it could be or is taking place. But Joel isn’t totally wrong to apply the bottleneck concept here. This sort of variation can’t go on forever. There’s a range of viable variation, and we may be reaching a completion of the spectrum.

      Like

      • 2 individuals equals 4 sets of everything, followed by recombination in forming the next generation. 4 sets of everyting is a bottleneck in genetic variation compared with the actual genetic variation found in nature.

        Liked by 1 person

      • “4 sets of everything” results in hundreds of millions of different sperm, not just the same “4 of everything.” You need to go read the paper I’ve referenced.

        Like

      • Hi Trevor, I agree that “4 sets of everything” is a bit simplistic but it not far off. With limited differences between the two homologous chromosomes you can have unlimited new variations in the sperm but what does that matter. Those differences will be so minuscule as to not matter much. No doubt a Dalmatian male makes a huge pool of unique sperm but that doesn’t create anything but more Dalmatians. Its not about combinations its about new useful differences that have a some reproductive fitness value – leaving aside genetic drift and population sizes for now. Before you say that a Dalmatian is at the end of the line of the sorting process, I will point out that we are going to differ on both how much variation that a single pair of individuals can contain and how much is necessary to produce offspring that can form amount of variations seen in the species that have come from them. Even if a super pair of animals could have a huge amount of variation this is also a question of likelihood not just one of remote possibilities. Every kind on the Ark would have to have these amazing amounts of genetic potential not just one pair. Sequences of ancient DNAs do not reveal that species from 1000s of years ago were all that different today. There should be some evidence of greater genetic potential in species of the past (not counting obviousy artificially selected organisms that do reduced genetic variation), if there the genetic entropy idea of Sanford really has any merit.

        Like

      • Hey Joel,

        Thanks for jumping back in. I must still maintain that the “4 sets” view really is quite far off. The huge variation in the sperm matters a tremendous amount; it can’t be overstated. If you read that paper I’ve been harping about, you wouldn’t say the differences would be “minuscule.” And as scientist we should deal with data, not assertions. The chromosomal differences noted in the paper are striking (aneuploidy for example would yield congenital disorders, and the SNPs could have very meaningful effects as well). Also, the Wang papers describes human genetic variation, but it could well be a species wide phenomenon. Thus every animal on the ark could have had this sort of variation potential.

        I think your statement about species looking the same now as they did 1000 years ago misses the point (and it would be helpful to know which species you’re referring to). The variation between the same species now and then is not the comparison that needs to be made. Ken Ham might suggest, for example, that a Giraffe was derived from a pre-Okapi. So it would be important to compare those species and ask if the necessary variation existed in the latter to derive the former. But saying that some species look the same now as they did then only proves that some members of the species didn’t diverge, not that no variation has taken place.

        But I think you make a good point about where our conversation is getting hung up. We disagree on how much variation an individual can have and how much is required for the changes we are discussing. To rectify this situation, we would need to know 1) which animals we are comparing, 2) which traits we are interested in, 3) what genes control those traits, and 4) what meaningful variants are known in those genes? Then we could make some comparisons and see what’s possible.

        Like

      • Trevor, 4 sets of everything never gives 5 of any gene. However you look at it, there is a genetic bottleneck. Recombination does not lead to any new alleles.

        Like

      • Hi Peter, please look at figure 5 in the Wang paper. You will find the refutation of your statement.

        Like

  10. The paper by Miller & Hedrick 2001 that Trevor refers to is relevant, but not whatever way Trevor thinks it is. Miller & Hedrick show that “the isofemale lines that did not show initial inbreeding depression declined in fitness after repeated bottlenecks, independent of the flush size”. That shows the animal populations deriving from the Ark woul have had lowered fitness. The Wang paper shows recombination – so what? recombination does not remove a bottleneck.

    Liked by 1 person

    • Yes, Peter. That’s part of the point I was making. A bottleneck might only result in slight reduction of sequence diversity (just rare alleles are lost in large quantities — See the PNAS 2006 paper I referenced); but you could still see an increase in speciation events according to Miller and Hendrick, even though the species’ fitness is reduced. I think this lines up well with the YEC perspective being discussed here. The ark bottleneck happened, speciation events increased and general fitness was reduced (at least in terms of human life span, and perhaps animal lifespan by extension).

      Like

    • As to the Wang paper only showing recombination “so what?” Recombination of the four parental alleles does not just produce four recombined alleles. It produces hundreds of millions of unique recombination events. This was not appreciated before the Wang paper because we always sequenced populations of cells rather than a single cell, so variation always looked far lower; It was diluted. Now we appreciate the true amount of variation that was there. Wang et al. also show that the recombination was happening in a very different way that previously thought. Its not just happening in large blocks in predictable areas. It happening in smaller regions as well and in highly variable hot spots. This is why there are so many variable haploid genomes produced, and its why the genetic variation is so high, and also why it can rebound after a bottleneck. It should also be appreciated that diversity could have been even larger in the animals on the ark since there were fewer historical bottleneck events. A bottleneck at that time may not have been all that catastrophic.

      Like

  11. Christine Janis says:

    Note the extreme rapidity with which the post-ark ruminant radiation must have occurred. Genesis 12.16 claims that Abraham already had oxen and sheep (not to mention camels and asses), so the entire diversity of modern ruminants (plus extinct forms) must have been accomplished in around a thousand years. That’s mouse deer (shown by genetics to be the basal form today), to ox, giraffe, moose, etc. in 200-300 generations.

    Liked by 1 person

  12. Hey, Jimmie,
    I’m with you all the way – from a conservative Lutheran side. I’d suggest Hebrews 11:3 telling everyone that WHAT WE SEE now is from “creatio ex nihilo” – not from anything SEEN by Noah’s contemporaries before the Flood. So trilobites and dinosaurs were not buried by the Flood (in that perfect order, remember). Instead of focus on DNA problems (as above) it would be easier just to look at the huge geologic deposition that had to happen post-Flood (as claimed by YECs) just to bury the dozens of major elephant species in the fossil record all post-Flood as Ham told Nye. Why not the creation of all such ecosystems (including all pre-modern humans) as God’s way of telling a holy humanity, “See how much more inventive I am, so trust me that I could have for you a more wonderful eternity than the life you live today.” All speculation, of course, but it makes sense. If you or anyone else wanted more, put together: gllemke – and then – @gmail.com. Not being computer literate, I have to make end runs. I did spend 1993-2013 on “time travel” back to 6000 B.C. (when you already had human ethnicities to provide wives for Noah’s sons in place) for a 99-scene Flood story starting at 6121 B.C., with 45 characters (many of whom missed the boat). Doing it with the geography of Turkey today in place pre-Flood, it ALL worked, zero suspension of disbelief. Even Ken’s Ark design is a wonderment of wasted space and impossible cleaning-up. Let Christians start with NO dinosaurs on board, and no problem. Just look AT their dino “tree” – one survivor gives you a dozen different species in time to suddenly go extinct? GLL

    Like

  13. Note to Jimmie — I’m with you all the way (except for the Old Earthism) in age and similar experience, and thank God for NH science vs. the unrealities of ICR & AiG. I spent 1993-2013 writing a Noah screenplay at 6000 BC, 99 scenes covering 150 years, zero suspension of disbelief, all questions answered. So yes, with 4 college summers ’93-’96 with USFS around Missoula, I could imagine a proper Ark constructed east of future Nicaea, needing geography of Turkey (and the world) the same as today post-Flood. With no cages (just 26 of 30 sections for free-range creatures) and no need for any fossil species, there’s room enough. The Morris 1976 Genesis sells an utterly unreal pre-Flood irrigation from below – and he was wrong to tell me that Job 28:25-28 isn’t about a created hydrology. The AiG “Ark Encounter” is worthless in every respect. “See how big it is!” doesn’t cut it.

    I’d like you and Christine and the rest to consider Hebrews 11:3 as a way out. How better could God have expressed this reality for people of a future that is now our present, than that WHAT WE SEE TODAY is all NOT from what was seen before the Flood, but from “creatio ex nihilo”? So coal and fossil bones aren’t from plants & animals living (SEEN) before the worldwide Flood. God’s perfect creation didn’t include an atmosphere loaded with carbon dioxide just waiting for plants to capture it all just in time for everything to be buried by the Flood to make coal and oil. Yes, everything today “looks old” just as it all looked old for Adam & Eve. What else would you expect but evolution’s big argument for “change through long ages” if ONLY GOD is unchanging and eternal, as he says?

    You and Christine could focus on Ken Ham telling Bill Nye that elephant “diversifying” happened post-Flood. This involves dozens of weird species found in geology of 5 or 10 or 15+ million years ago in Deep Time – all of which had to be “deposited” post-Flood. And elephant growth to maturity doesn’t happen in a few years. I wish Trevor could deal with this before so much argument about genes and DNA. It gets even worse, with Grube Messel (a world-class site) in Germany also full of post-Flood creatures – a very long hike from the Ark landing in SE Turkey, 200 miles south of Ararat. Since German geology is also “Flood-deposited” under Messel, they have to argue post-Flood.

    Not being computer literate (except for finding things like “Etna 6000 BC” on Google, and of course NH giving us Carbon-14 from Lake Suigetsu), I can still encourage you and anybody to get in touch for private conversation at: gllemke — and then — @hotmail.com. We’d talk about things like the Chesapeake Bay Impact also an impossible Flood-time event. And I’m always looking for details that others can fill in for me. Consider how, if the Hawaiian Islands are also post-Flood (Snelling, AiG), with the Pacific & American plates heading west, then ALL of ICELAND is post-Flood (!). No way.

    Like

  14. Hey All – Sorry about the double entry (above). I did the first from the library downtown last night, and it looked like it didn’t go through, and this morning it wasn’t there, so when I did “Post” of what I wrote this morning, BOTH suddenly popped in, to my surprise. I might mention for Jimmie that I also was voted out of my conservative Lutheran parish 4+ years ago for being “divisive” (telling everybody for too long that: No, dinosaurs on the Ark is a bad idea). You might look into Lutheran Science Institute for a major questionnaire – where 12% of respondents were OK with created dinosaur bones (but then almost everybody favored a later “Did the Flood do it all?” question). So now I’m waiting for this fellowship to get back to me on Hebrews 11:3 — and, of course, 2 Peter 3:6 telling us FIRST OF ALL about people being destroyed (as again at 3:7b). “Kosmos” in 3:6 is the same as the “kosmos” in John 3:16 (and some 150 other “people” verses in the New Testament).

    Like

  15. Reblogged this on New Horizons and commented:
    The absurdities of Ken Ham and “Creation Science.”

    Like

  16. Roger Boltz says:

    This is very well-reasoned and makes perfect sense. The problem with these endless arguments that try to resolve the Bible with modern science is that both sides assume a cosmology that is both materialistic and uniformitarian. In other words, our reality only unfolds according to fixed laws observable in nature, and those laws can never change throughout the history of the cosmos. I believe this is a trap. (Albeit one to which the cutting edge of modern physics May hold a key.)

    The Bible makes straightforward claims that events took place, without offering scientific explanations as to how they were accomplished. If Christians get entangled in the pop science trap, either we must postulate a scenario that conforms to Modern scientific observation, or we must craft a hermeneutic that allows the Bible to be true without requiring it’s literal sounding claims to be taken as such. How about this one…

    A man’s body is lacerated almost beyond recognition, he is suffocated by crucifixion, and most of his blood is drained in front of hundreds of witnesses. After three days and nights lying in a tomb his cells regenerate, his wounds heal, and he rejoins his companions, not as a spirit but as flesh and bone, eating and drinking with them.

    There is no possible scientific explanation, but if it didn’t happen, we don’t need to be having this conversation. In quantum physics, all future realities are just possibilities with varying degrees of probability. With God, all things are possible.

    Like

    • Roger, we have absolutely no evidence that uniformitarianism is incorrect. For your argument to be correct, you have to assume that the scientific laws inexplicably changed in such a way as to be perfectly consistent with each other afterwards, but which would contradict the biblical account. Why would this happen?

      Like

      • Roger Boltz says:

        Good question! I don’t necessarily assume that “scientific laws” change; I simply don’t see them as immutable “laws.” They are nothing but observed consistencies in the default behavior of material systems. Many physicists have deduced that those DNA molecules are made up of atoms, which are made up of protons, neutrons and electrons, which are made up of six varieties of quarks, which are themselves but manifestations of various resonances (string theorists call the locuses of these resonances “strings”) between the four dimensions of spacetime that we observe directly and the other dimensions (perhaps 7) that we do not.

        Some would further postulate that at the quantum level, all “particles” of matter come into and out of existence–are “instantiated”–at an oscillation frequency related to the Plank time (10^34 instantiations per second for example.) Finally, given the location and status of a “particle” in the present “instant”, there are virtually infinite possibilities for its location and status in the next instant, each possibility having its own probability. If a particle is incorporated in an “observed” structure–say an electron in the K shell of a carbon atom in a DNA molecule–then the possibility that it will in the next instant appear very close to its location in the present instant has the highest probability… but never 100%. In general, the observed consistencies we call “scientific laws” will determine the probabilities of possibilities, but other factors may have unexpected influence, including one’s own consciousness and intention. A much more profound and dramatic influence may be exerted by the conscious intention of the Creator.

        If you’re still reading after those two admittedly convoluted paragraphs, then here’s my argument. The resonances of those strings are the voice of God speaking into existence the possibilities of His imagination–the Word of God–according to a set of probabilities that manifest the Will of God. Once spoken, those words of the Creator are kept in motion unfolding in the direction He sent them by the Faithfulness of God… which includes the observed consistencies we call “scientific laws.” If we catch Him in the act of speaking a word that transcends those “laws”, we call it a miracle. If we were not present to observe such a miracle, we presume to our peril that we can prove by those “laws” that it could not have happened as recorded.

        Was that even intelligible? It’s two in the morning…

        Like

  17. Hi, Thanks for the insightful critiques of YEC scientific literature. A related problem for the genetic bottleneck is the environmental bottleneck. It is difficult to imagine less favourable conditions to reach sustainable populations for biodiversity. Starting at the base of the food chain: the lack of primary production in a world covered in mud, debris and presumably salinity (anything else?), intense competition between herbivores, animal predation. The aquatic life wouldn’t have fared much better. According to the AiG model, trillions of tonnes of soil, nutrients and organic matter would have entered the oceans. We know from observational environmental science in the present the devastating effects of habitat destruction and water pollution on ecosystems.

    Liked by 1 person

  18. I was pretty astonished reading Trevor’s posts so I decided to go through the sources he cites and read the papers to see what they say.

    “Moreover, although the ark bottleneck was extreme, Miller and Hendrick (J. Evol. Biol. 14[2001]595-601) suggest that it’s not the magnitude of the bottleneck that results in the loss so much as the pattern of recovery afterwards. This of course highlights that recovery of variation after a bottleneck is a reality, but you don’t mention that anywhere in your post.”

    “Purging of inbreeding depression and fitness decline in bottlenecked populations of Drosophila melanogaster”: This paper took female wild fruit flies, ran their offspring through three generations of full-sib mating, grew up the population, and sorted them by inbreeding depression. These different inbred strains were then subjected to repeated bottlenecks. They ran two parallel experiments, one in which the population was allowed to rebound between bottlenecks, and one in which the population number was kept low between bottlenecks.

    This experiment DID NOT show recovery of genetic variation, like Trevor stated. It showed that repeated bottlenecks are capable of increasing population fitness. To quote the authors, “the set of detrimental alleles primarily responsible for lowered fitness from inbreeding or bottlenecks may be effectively purged by the combination of genetic drift and/or inbreeding and selection.” The fitness of some of these inbred strains increased through repeated bottlenecks because of the purge of detrimental alleles from the gene pool. This is, of course, nothing new. We know, as I believe you mentioned, that some highly inbred populations may be well adapted to their environment and thus highly fit. To illustrate this, consider the bdelloid rotifers that alternate between asexual and sexual reproduction. In ideal conditions (where the rotifers are adapted and fitness is high) rotifers produce asexually and grow rapidly to large population sizes. When conditions change and the population experiences stress (that is, fitness is decreased), they switch to sexual reproduction. Sexual reproduction allows recombination of alleles. This results in shuffling of alleles to combinations that may be more ideal for the new conditions, and also the segregation of detrimental alleles into unfortunate individuals who are highly unfit and are eliminated, thus reducing the frequency of detrimental alleles in the population.

    “Bottlenecks are most harsh towards rare variants but keep the sequence diversity largely intact (here’s one example: Proc Natl Acad Sci U S A. 2006 Nov 7; 103(45): 16666–16671).”

    “Impacts of genetic bottlenecks on soybean genome diversity”: What are Trevor’s criteria for sequence diversity being “largely intact”? And does he believe the results of this study generalizable to all bottlenecks?

    In this study they compared the diversity in the wild ancestor to domestic soybeans, Asian soybean varieties, the North American varieties drawn from a small number of Asian soybean cultivars, and “elite” strains that are commercially farmed in North America today. They found the biggest reduction of genetic variation at the domestication bottleneck “when the low sequence diversity present in the wild species was halved, 81% of the rare alleles were lost, and 60% of the genes exhibited evidence of significant allele frequency changes.” Going from the Asian cultivars to the North American ones, there was no statistically significant change in diversity measured by pi (“expected heterozygosity per nucleotide site”) and theta (“number of polymorphic sites in a geotypic sample corrected for sample size”). However, there was a 78% loss of low-frequency alleles.
    The authors note several explanations for the limited reduction in diversity from Asian to modern commercial cultivars that the soybean ancestor has an unusually low amount of genetic variation itself, as a major crop historically soybean probably maintained a high population level, the requirement that soybean grow in the US in a wide vareity of conditions encouraged maintenance of diversity, and much of the genetic variation in soybean may have been neutral and been spared artificial selection.

    I will note that while Trevor is correct in saying variation did not change much from Asian to North American cultivars, it was reduced by about 1/2 during domestication, so clearly bottlenecks do not “keep the sequence diversity largely intact”.

    The development of North American soybean cultivars is not generalizable to all population bottlenecks–especially those where a population is reduced to two individuals.

    “Going further, single cell DNA sequencing in the last 4 years (Cell. 2012 Jul 20; 150(2): 402–412) demonstrates how this variation is represented intact across hundreds of millions of astonishingly heterogeneous sperm from a single donor (this variation was previously masked by genetic analyses of sperm populations rather than single cells). ”

    This paper seems to be the keystone of Trevor’s argument. He says that we are mistaken about the amount of genetic variation an individual can pass along. Supposedly individuals are really capable of passing along tremendous amounts of variation, and this was the source of hyper-evolution to produce modern species.

    If this is the case, and this genetic variation is preserved in every individual, why is hyper-evolution not continuing right this second? Why do we not see “hopeful monsters” springing forth constantly? Where are the large numbers of speciation events, and offspring radically phenotypically different from their parents?

    Well, I read the paper and it looks to me like much ado about nothing. As the paper states time and again, we have population-level data on the phenomena they are examining (recombination and mutation). What this paper does is zoom in on one individual and check for recombination hotspots and whether the individual’s mutation rate is in line with the population average. Regarding recombination, they have an entire section entitled “Personal Recombination Map Recapitulates Population Results at a Broad Scale”. No big surprises there. I will quote a little more because Trevor stated in one post that the individual studied had radical new recombinations: “Taken together, P0’s personal recombination map shows that recombination events within an individual recapitulate the general broad-scale features from population data. Our results experimentally demonstrate general concordance between an individual and the population average, which can be thought of as an analogy to the ergodic principle from statistical physics.” The individual studied had some recombination sites that seemed to be favored when generating sperm, but these were sites observed already in the larger population. His mutation rate was also slightly larger than the population average, which is consistent with evidence that shows men have a higher mutation rate during gamete production than women. (My speculation: and possibly is age-related? The donor was 40).

    So, no, an individual does not have “infinite genetic potential”. Recombination does not produce new alleles, it shuffles existing alleles into new combinations. Mutation can produce new alleles, but as geneticists have observed already, this is a small minority of mutations. Most of the mutations they observed were intronic or intergenic. Trevor will say “alternative splicing!” and “transcription regulation!”, but we know from previous studies that most of these mutations do nothing and have no observable impact on gene expression.

    Trevor also seems suprised at the high rates of aneuploidy (I invite any explanation of the difference between “missing entire chromosomes” and “whole-chromosome aneuploidy”), but this was already known. The authors mention the high rate of so-called “chemical pregnancies” where the embryo dies soon after implantation. Aneuploidy is thought to be a major cause of this.

    Our learning more fine detail on gene expression and variability does not negate previous large-scale findings of geneticists studying genome diversity. Those studies do not support “infinite genetic potential” and hyper-evolution.

    Liked by 2 people

    • Great work. Thanks for your persistence in looking at the article carefully.

      Like

    • I am inclined to agree with your observations Petrel, although you make as many good points against Trevor as you do Darwinian evolution. And may I suggest that the reason we don’t see “lots of hopeful monsters” is because we don’t see any at all. And the reason we don’t see “hyper” evolution is because we don’t see any evolution, at least of the macro type, which may answer your inquiry about speciation events and radical phenotypical changes. Good post, though.

      Like

      • If there is no evolution, then obviously there can be no ‘hyper evolution’, so how did all of the species diversify after the flood?

        Like

        • Mega, you’ve got to remember that all the different perspectives can mean something different when they use the same terminology. I doubt the yec EVER mean evolution in the Darwinian sense. Progressive creationists can and do, but allow for divine intervention, but mostly at the beginning. i’m sure you know that yec allow for micro but not macro evolution. And they accept natural selection, at least in it’s most general meaning. And of course, specie “change”. ID, of course, believe that however it occurred, it was by design. I think you’re question is better directed at the progressive creationist (or theistic evolutionists as sometimes called). They believe in Darwinian type evolution, but not really. Darwin did not allow for divine participation at all. This is why progressive creationist can’t seem to find a home anywhere. They are too Darwinian for YEC, and also ID. ID is too vague for YEC, and not Darwinian enough for theistic evolutionists. It gets confusing. Believe me, HAM and the YEC do not mean Darwinian evolution when they say “evolution”. They more likely are referring to natural selection, and variation. As for progressive creationists, you should ask them. Although they are theistic, I find their perspective the most fraught with inner contradictions and difficulties.

          Like

          • That still doesn’t answer the question of why this YEC hyper evolution isn’t occurring today. the YEC HE hypothesis requires significant change over a far shorter time-scale than the theory of evolution does, so regardless of how you define evolution, if there is no standard evolution, there is no hyper-micro-evolution either.

            Like

            • well, I suggest you read their literature, and of course, counter positions. Change does not equal evolution, not in the Darwinian sense. As I said, from a yec point of view, one is free to envision the activity of God in all process at any time. Not so for all other counter-vailing perspectives. If, in a sense, you are asking why you don’t see what you think you should see, it may be because you are looking for something that doesn’t exist in their paradigm, therefore they don’t have the “need” to explain what is irrelevant to “them”. You use the phrase “hyper-evolution”. Trust me, if you are not YEC, then you mean something different, even contrary, to what they believe. YEC “evolution” is merely change within species, variation. If, when saying “hyper-evolution” you are envisioning some “sped-up” version of Darwinian evolution, then you are both misunderstanding and misinterpreting what they are saying. Thus my point in previous post. When four or five perspectives use the same or similar language but mean something different or opposite, there’s no wonder why so little is accomplished in dialogue. As long as you don’t agree with them, or their definitions, little will be accomplished. You are at most relegated to critiquing the consistency of their argument, not whether it passes muster with your own.

              Like

              • But whether you consider evolution to be change within species or transitions between species, there is no explanation for why the process (in the YEC paradigm) has suddenly slowed to a comparative crawl.
                It can’t be that species have simply reached the end of their mutability or genetic variation, as we still see such changes occurring today. But if the YEC position is correct, then either the hyper adaptations would be continuing as we speak or something major would have happened to prevent it.

                Like

                • I guess my next question for you is “what exactly do you a hyper adaptation”. What is it (give an example) and why do you consider it a “hyper” type of adaptation? And again, seeing as how YEC allow for God’s “presence” In the process, manipulating or changing parameters, they could explain that the “evolution”(remember, they don’t mean Darwinian) was “hyper” only and as long as God designed it to be. And while I agree we “see” changes today, we don’t see anything of a Darwinian type. There are no “leaps” (nature doesn’t jump), just small incremental changes that one would expect with the vast variety inherent in genetic makeup. There are no amphibian to reptile to mammal to human “leaps” required indarwinian belief. And seeing as how Darwinian evolution has been going on, one assumes, for 100’s of millions of years, I’m not exactly clear on what would qualify as a “comparative crawl”? Now understand I am not defending yec doctrine, just merely trying to understand and explain what I have surmised. Seeing as how Gould et al came up with punctuated equilibrium to justify huge non-Darwinian like leaps in the evolutionary process, it becomes harder to discern clearly exactly WHAT one should look. A hopeful monster, perhaps? If a process is so slow that it takes 500 million to one billion years to occur, at what point could it be considered hyper and would anyone live long enough to even observe such a thing?

                  Like

                  • By hyper adaptation/evolution, I mean the diversification of the vast number of modern species from the proposed original ancestors that the YEC group offers up in just a few thousand years, as opposed to those groups (such as all felines, or all canines) having their common ancestor millions or tens of millions of years ago, as the genetic and fossil evidence indicates, which is what I mean by a comparative crawl. If all of our tens of millions of species today came from a few thousand original ‘kinds’ within a few thousand years, why do we not have thousands of new species popping up every day?
                    If you add in God’s presence to explain any anomalies or change parameters at will without leaving any evidence behind, then there’s absolutely no point in trying to explain it scientifically in the first place.
                    Gould came up with punctuated equilibrium because it better explains the data than gradualism. It wasn’t done to ‘justify’ anything, just explain the pattern of fossils.

                    Like

                    • i understand both your viewpoint and concerns. As Ham et al make their own proposals, i will leave it to them to explain them. Thus you must search their writings. I merely seek to make you aware of differences in meanings often applied to the same words. And seeing as how they do allow for divine intervention (I’m not saying that they “slip” God into every difficult to explain area), then obviously you and they will not ever agree on many things, no matter how voluminous the explanations may be. You would do best to read their own material, and not rely on someone else’s summation of it.

                      Like

                    • Fair enough.

                      Like

  19. Christine Janis says:

    Chuck said: “Seeing as how Gould et al came up with punctuated equilibrium to justify huge non-Darwinian like leaps in the evolutionary process,”

    No he didn’t (and it was Eldredge and Gould, not “Gould et al.”). Punctuated equilibria (not a typo) was originally proposed to explain the lack of transitional forms between species (within genera) in marine invertebrates. Why you see trilobite species a, then trilobite species b, without intervening trilobite species ab. And it was also to note that species tend to remain the same for a long while, and then are suddenly replaced — rather than evolution proceeding at a single steady rate.

    Eldredge and Gould explained this phenomenon being due to speciation taking place in small areas outside the range of the main population (and hence unlikely to be fossilized), with species b then replacing species a. Most people today think that this phenomenon is the result of an imperfect fossil record, and in places where there is a continuous sequence (e.g., the Bighorn Basin in Wyoming) gradual change from one species into another (this time early mammals) can be documented.

    However, it’s still true that stasis may be the rule in evolution, and when change happens it tends to affect a bunch of taxa in a community together — probably reflecting environmental change.

    Liked by 2 people

    • well, a familiar voice. face? writer? Anyway, you took 200 words to say what i said in 15. Gould et al referred to, yes, Eldridge and Gould, and any and all who took to their hypothesis, though many didn’t. Punctuated equlibria (there, feel better now?) isn’t, from a philisophical standpoint, terribly different from “God in the gaps”, just another appeal to a hypothetical source for a process unobserved or otherwise unexplainable, i.e., where are the transitional fossils? Remember, evolution don’t do no jumpin!” With hundreds of millions of recovered fossils, it seems a bit desperate to appeal to an imperfect fossil record. For Darwin, yes. Now, doubtful. I realize PE sounds more scientific than “hopeful monster”, but we are still left with the same dilemma, no matter what we try to fill the gaps with. As to your “no he did-int”, i’m not sure why eldridge and gould is vastly different from Gould et.al.? Are we back to nit-picking again? Did you mean to imply that Gould was not involved? More than just Gould? (thus my et.al.). Why was that even important? Don’t worry, I know why you “made the point”. Good ole Christine. I’ve missed you so.

      Like

      • Christine Janis says:

        “Anyway, you took 200 words to say what i said in 15.”

        What you said in 15 words was incorrect, so it took more words for me to correct it.

        PE is not about saltation – it is about the tempo of evolution. And, as I said, in the rare cases when the fossil record is good enough gradual change between species of a genus can be observed. This is quite different from so-called the “missing transitional fossils” between taxa above the species level that creationists claim are absent which, as Gould himself noted, are there in abundance (and many more have been discovered since his death).

        Here is an example to make the point. The fact that the Solenhofen limestone contains two species of Archaeopteryx, A. lithographica and A. bavarica, but no individual fossil intermediate between the two, does not mean that Archaeopteryx is not a “transitional fossil” between theropod dinosaurs and birds.

        “it seems a bit desperate to appeal to an imperfect fossil record.”

        It would be impossible, in terms of earth history — which includes such physical events as erosion, plate tectonics, and the fact that the sea covers the majority of the globe — for there to be a geological record that preserved every layer of every stratum, from Hadean to Holocene, in every place — each place accessible to geological investigation. So, even if every individual that died had originally been preserved, there is little hope of the fossil record ever being complete. But it is indeed better than in Darwin’s day. For example, we now have a fossil record from the first 7/8th of earth’s history.

        ‘Don’t worry, I know why you “made the point”. ‘

        To set the science straight, while resisting the temptation to be snarky? (I will, however, point out that you spelled Eldredge wrong. Precision is important in science.)

        Liked by 2 people

        • actually christine, you didn’t “correct” anything. You just gave your opinion, unless, of course, you assume that your opinions are always correct, which i believe you do. And switching from an “incomplete fossil record” to “an imperfect” is nothing more than changing terminology as an artificial “fix” for a pervasive, persistent, and permanent problem with the fossil record. To appeal to lack of evidence as evidence of no “lack” is clever but disingenuous and vacuous reasoning. When a theory cannot be falsified it should no longer be considered, and that’s what you (et. al.) are doing when absence of evidence is actually explained away as some sort of reasonable proof of said theory’s validity.
          the phylogenetic trees used by evo’s are missing far more than a twig or flower bud here and there. There are enormous gaps. Especially when imagination is removed and replaced by only hard, existent fossil proof. Gould aside, who often fluctuated between clear honesty about the fossil record (much to his colleagues chagrin) and the alice in wonderland visions of hopeful monsters, let’s be clear. There are lots and lots of fossils, and many of them are similar to other fossils. Some evidence minor changes. (microevolution or variation). There are no known irrefutable transitional fossils required by darwinian evolution (macro). If the ultimate appeal is to unknown hopeful monsters and a fossil record that will never be complete(conveniently), then you’ll excuse my less than enthusiastic embrace of evolution.
          And may i take the time to remind you that until evolutionists can explain how the infinitely impossible happened (the spontaneous generation of life, and sorry, saying it must have occurred because it occurred is simply little more than dicto simpliciter and begging the question), or how mutations can add beneficial information trillions upon trillions of times when observation shows otherwise, then i am afraid that getting all goose-bumpy over slight variations (not transitions) in the incomplete fossil record is, as i have stated previously, a bit like debating what color a unicorn is. Much ado about nothing. If you want to embrace a hypothesis, chose one that both withstands and answers all challenges. Precision in science isn’t just important, it’s everything.

          Like

          • Christine Janis says:

            Chuck — if you want to play with the big boys and girls, learn something about the science first and resist presenting a cartoon version for self-destruction.

            Liked by 1 person

            • look Christine, it’s not my fault if you adhere to a particular paradigm absent of any empirical (science is precise, right?) evidence. Nor do you do yourself any credit by resorting to the usual and predictable “well, if I can’t refute the other point of view, I’ll just make pejorative remarks about the person holding the view.”
              And again, your remarks reek of the arrogance and condescending traits that you and many evolutionists display. I often wonder if the cry for “better understanding of the science” isn’t actually a plea from those like you who themselves have little comprehension of their own beliefs, primarily, I imagine, because you accepted what you were taught like a two-year old accepting a spoon of mushy stuff. No real discernment, no questioning, just rote repetition of religious creed hiding in the guise of science. And always, always, with the above revealing traits, no real answers or refutation of any challenges or objections to your doctrine. And finally, as I mentioned before, the arrogant assumption that whatever YOU belief, is of course, what everyone should believe, apparently oblivious to the reality that the most damning objections regarding Darwinian-evolution often come from evolutionists (and not just former, but quite often current) themselves.
              In addition, you seem to have little or no apparent knowledge about the history of science or philosophy of science. You seemed to have learned little from your “whippo” debacle, but denial and delusion often go hand in hand. I’ve offered to let you move on, but you insisted on being humiliated, then appeared to disappear for awhile when, on another thread, whippo became a topic of conversation.
              If humiliation is what you lust for, I would offer you more, but, as experience shows, you are capable of little more than name-calling and an incredible talent for denying anything that displeases you, though the history books may be overflowing with authentication of said topic. The unfortunate thing is that few if any of your cohorts are willing to correct you, either because they fear your insulting wrath or wish to remain blissfully, albeit mistakenly, incorrect. Do not take this silence as an endorsement of your viewpoint. It means nothing. And try to stop pretending that evolution is some God-awful complicated theory that only the high priests of science can understand. It’s simply a mish-mash of contradictory ideas or events that have never been proven to have occurred, or the same but with alternative explanations not beholden to Darwin or his sychophants. When the best retort you can offer consists of correcting one letter in a name, or offering irrelevant examples not even pertinent to the discussion, well now you know why I am so underwhelmed by you. Perhaps you should go edit a science book. Here’s a suggestion, while doing so actually check to make sure you editing something true.

              Like

          • The theory of evolution could be falsified very easily. All you need is a fossil that is unambiguously in the wrong strata. If it turned out that there was no evidence of chromosomal fusion in human ancestry then the theory of evolution would have been falsified. However, this was predicted and later confirmed. Evolution is testable and falsifiable, whereas ID is not.
            Gould’s comments on the fossil record have frequently been, shall we say, ‘edited’ by creationists.
            For example:
            “The extreme rarity of transitional forms in the fossil record persist as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils ….We fancy ourselves as the only true students of life’s history, yet to preserve our favored account of evolution by natural selection we view our data as so bad that we never see the very process we profess to study.” – Stephen J. Gould – “Evolution’s Erratic Pace,” Natural History, vol. 86 (May 1987), p. 14.

            The full quote, however, goes like this:
            “The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils. Yet Darwin was so wedded to gradualism that he wagered his entire theory on a denial of this literal record:
            ‘The geological record is extremely imperfect and this fact will to a large extent explain why we do not find interminable varieties, connecting together all the extinct and existing forms of life by the finest graduated steps. He who rejects these views on the nature of the geological record, will rightly reject my whole theory.’
            Darwin’s argument still persists as the favored escape of most paleontologists from the embarrassment of a record that seems to show so little of evolution [directly]. In exposing its cultural and methodological roots, I wish in no way to impugn the potential validity of gradualism (for all general views have similar roots). I only wish to point out that it is never “seen” in the rocks.
            Paleontologists have paid an exorbitant price for Darwin’s argument. We fancy ourselves as the only true students of life’s history, yet to preserve our favored account of evolution by natural selection we view our data as so bad that we never see the very process we profess to study.
            For several years, Niles Eldredge of the American Museum of Natural History and I have been advocating a resolution to this uncomfortable paradox. We believe that Huxley was right in his warning. The modern theory of evolution does not require gradual change. In fact, the operation of Darwinian processes should yield exactly what we see in the fossil record. [It is gradualism we should reject, not Darwinism.]”

            If we look at some more of his quotes, we see a similar pattern:
            “Transitions are often found in the fossil record. Preserved transitions are not common — and should not be, according to our understanding of evolution (see next section) but they are not entirely wanting, as creationists often claim. [He then discusses two examples: therapsid intermediaries between reptiles and mammals, and the half-dozen human species – found as of 1981 – that appear in an unbroken temporal sequence of progressively more modern features.]
            Faced with these facts of evolution and the philosophical bankruptcy of their own position, creationists rely upon distortion and innuendo to buttress their rhetorical claim. If I sound sharp or bitter, indeed I am — for I have become a major target of these practices.
            I count myself among the evolutionists who argue for a jerky, or episodic, rather than a smoothly gradual, pace of change. In 1972 my colleague Niles Eldredge and I developed the theory of punctuated equilibrium. We argued that two outstanding facts of the fossil record — geologically “sudden” origin of new species and failure to change thereafter (stasis) — reflect the predictions of evolutionary theory, not the imperfections of the fossil record. In most theories, small isolated populations are the source of new species, and the process of speciation takes thousands or tens of thousands of years. This amount of time, so long when measured against our lives, is a geological microsecond . . .
            Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists — whether through design or stupidity, I do not know — as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups.
            – Gould, Stephen Jay 1983. “Evolution as Fact and Theory” in Hens Teeth and Horse’s Toes: Further Reflections in Natural History. New York: W. W. Norton & Co., p. 258-260.

            As for beneficial mutations, we see it all the time.
            First there is the E coli experiment performed over several decades by Dr Richard Lenski and his team of researchers in their notable Long-Term E coli Experiment (which is possibly the epitome of a good scientific experiment). Starting out with twelve initially identical strains, after several decades of depleted/replenished food supplies (the sugar glucose) the strains were all very different from each other, despite starting out from the same sample. The laboratory strains contained no less than nine mutations which helped them adapt to their new feast/famine environment and could grow 70% faster than they had at the beginning of the experiment. One of the strains was twice as big as it used to be and had developed the ability to metabolise citrate in aerobic conditions. This gave it an immense evolutionary advantage as it allowed the strain to grow to twice the population size of the other strains. Regular samples were frozen, allowing the researchers to have literal living fossils that they could thaw out and analyse, which they did, allowing them to pinpoint when the mutation occurred to within a few hundred generations (out of tens of thousands). Several beneficial mutations reached fixation. Note that this experiment shows how mutation can provide beneficial traits, and is not about speciation.
            http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430337/
            http://www.pnas.org/content/105/23/7899.abstract
            http://www.researchgate.net/publication/258115839_Genome_dynamics_during_experimental_evolution
            http://www.nature.com/nature/journal/v461/n7268/abs/nature08480.html

            Another experiment involving E coli was that conducted by Dr Barry Hall and his colleagues at the University of Rochester, when they deleted a particular gene from a strain of E coli and released it into an environment that contained lactose as the only food source. The problem was that the gene they had deleted was the one that allowed the E coli to break down the sugar into subunits for food via an enzyme. Because they couldn’t break down the lactose the E coli initially couldn’t grow, but very quickly a mutation arose that allowed a different enzyme to break down lactose, where it couldn’t beforehand, although this new enzyme wasn’t nearly as efficient at it as the old one. Some time later a second mutation arose that allowed greater quantities of this new enzyme to be produced, meaning that more lactose could be metabolised and that the bacteria could therefore grow faster. A third mutation (which arose in a different gene) allowed the E coli to take up lactose more easily. So we have an observable, repeatable experiment showing the evolution of a complex biochemical pathway in a short period of time, due to nothing more than mutations and natural selection. Argue that one, Behe.

            We can even see the origin of new, ecologically diverse bacterial species, all within a single laboratory flask. Paul Rainey and his colleagues at Oxford University placed a strain of the bacteria Pseudomonas fluorescens in a small vessel containing nutrient broth, and simply watched it. (It’s surprising but true that such a vessel actually contains diverse environments. Oxygen concentration, for example, is highest on the top and lowest on the bottom.) Within ten days—no more than a few hundred generations—the ancestral free-floating “smooth” bacterium had evolved into two additional forms occupying different parts of the beaker. One, called “wrinkly spreader,” formed a mat on top of the broth. The other, called “fuzzy spreader,” formed a carpet on the bottom. The smooth ancestral type persisted in the liquid environment in the middle. Each of the two new forms was genetically different from the ancestor, having evolved through mutation and natural selection to reproduce best in their respective environments. Here, then, is not only evolution but speciation occurring the lab: the ancestral form produced, and coexisted with, two ecologically different descendants, and in bacteria such forms are considered distinct species. Over a very short time, natural selection on Pseudomonas yielded a small-scale “adaptive radiation,” the equivalent of how animals or plants form species when they encounter new environments on an oceanic island.

            We know that the size of an organisms genome can increase through gene and genome duplication, copying the gene or genome and sometimes even doubling the size of the genetic information, which mutations can freely act upon.
            http://www.sciencedirect.com/science/article/pii/S0169534703000338

            Liked by 1 person

            • thanks mega for all that hard work. I appreciate the time you took to do it. I might counter both yours and Gould’s claim to the effect that he was, so to speak, “grossly misquoted”. Neither the “creationist” quote nor the fuller version give any thing resembling a ringing endorsement of the fossil record. The latter seems to present an opportunity to vent bile at creationists. Neither statement answers the fault found in the fossil record, lack of substantiation. He seems, in fact, to be begging the question, i.e., the reason we don’t find the fossils we need to find is because we shouldn’t expect to find the fossils we are looking for. This answers nothing, nor does anything in his fuller statement strengthen the case for the fossil record.
              As to the lab experiments, fascinating but inconclusive. Mutations occur. Variations occur. I think that is accepted by now. Still, it doesn’t bring us to where we need to be. Adaptation is observed. That is, when mutations aren’t lethal. Why do so few ask the elephant in the room question. What we are observing is intelligently designed experiments. By intelligent designers. One must never remove that critical and crucial element. While possible, it might be a huge mistake to assume that what we manipulate in the lab might not be an exact representation of what is happening out there in that wild, random, chance world.
              Nonetheless, thank you for taking the time. I read it all and checked the links. I love science and always enjoy the opportunity to learn new info or keep updated on current studies. I do not, however, read the research as does, say, a muslim reads the Koran. What is sacrosanct today may be heresy tomorrow. Still, I love the journey. Thanks again. Always enjoy your posts.

              Like

          • Christine Janis says:

            I wasn’t going to directly respond to this, but there are a couple of items.

            “Actually christine, you didn’t “correct” anything. You just gave your opinion,”
            I provided a correct description of what the theory of Punctuated Equilibra is actually about, which you had entirely wrong. That is not “my opinion”, it is the fact of the matter.

            “And switching from an “incomplete fossil record” to “an imperfect” is nothing more than changing terminology as an artificial “fix” for a pervasive, persistent, and permanent problem with the fossil record. ”
            This simply hilarious, because you were too busy with your enraged mansplaining to notice that what I was doing was quoting your own words. Which is why that sentence in my reply is in quotes.

            Like

            • You are the funny one, Christine. I imagine that your counselors there in the asylum probably might make sense of the later part of your reply, but as for myself, I think you’ve devolved into a debate with yourself.
              As for punctuated equilibrium, I quite understand what Gould believed, or came to believe, it was. And his tendency to move away from gradualism (translate: uniformitarianism), which had become the adhesive that held all things Darwinian together. As for your above references about transitional series of feathered dinosaurs, what exactly is it about them that makes you think they are “transitional” and not just variation. What advantage would feathers give a creature living in the seas? Or a dinosaur for that matter. Just what is the advantage (remember, we need that). Unless the fish immediately went airborne, joined by Rex, his dinosaur friend, what is it that motivates you to see these variations as advantageous rather than deleterious? And all the while we are assuming that the “feathers” are actually feathers.
              And as usual, you never, for whatever reasons (fear I suspect) mention that there are other viewpoints, within evolution, concerning these discoveries. Now of course, you are under no obligation to do so, but it does make me suspect that you are rarely even aware of this. Even though such disagreements do no significant damage to study of evolutionary theory, I get the feeling that you personally need everything regarding evolution to be “just so”. Which is why, by the admission of quite a few evolutionists themselves, much of evolutionary theory consists of “just so” stories. They are embraced “just so” Darwinian believers can continue on their incredible journey. Your replies are repugnant, and you impress no one but yourself (and perhaps, members of your immediate family, who, I’m sure, are kind and wonderful people).

              Like

  20. Christine Janis says:

    Megasolipsist quoting Gould: “We argued that two outstanding facts of the fossil record — geologically “sudden” origin of new species and failure to change thereafter (stasis) — reflect the predictions of evolutionary theory, not the imperfections of the fossil record. In most theories, small isolated populations are the source of new species, and the process of speciation takes thousands or tens of thousands of years. ”

    The critical thing here is the word species. I know that creationists like to use the term “species” to mean any taxon of interest, but this is not what Gould was talking about . Related species within a genus, or perhaps even related genera —- nothing to do with saltation, and nothing to do with the transformation of one kind of animal into another (except, of course, that over time it’s all just speciation).

    “Transitional forms are generally lacking at the species level, but they are abundant between larger groups.”

    And remember that Gould was writing this before the discovery of the transitional series of feathered dinosaurs and fishapods.

    Liked by 1 person

  21. Christine Janis says:

    Chuck said: “You are the funny one, Christine. I imagine that your counselors there in the asylum probably might make sense of the later part of your reply”

    You mean the fact that you objected to my using the word “imperfect” when I was quoting your own words.

    Meanwhile, I guess that you must be braying so much about how deluded the lady scientist is because she handed your ass to you.

    Liked by 1 person

  22. Christine Janis says:

    @ Chuck :As for your above references about transitional series of feathered dinosaurs, what exactly is it about them that makes you think they are “transitional” and not just variation.

    Lots of features about their anatomy — something that you could certainly google if you were really interested.

    “What advantage would feathers give a creature living in the seas? ”

    A strange question. Although I note that penguins retain feathers.

    “Or a dinosaur for that matter. Just what is the advantage (remember, we need that). ”

    We do indeed. Why do you think that ostriches have feathers. despite the fact that they do not fly?

    “Unless the fish immediately went airborne, joined by Rex, his dinosaur friend, what is it that motivates you to see these variations as advantageous rather than deleterious? ”

    Unintelligible argy bargy.

    “And all the while we are assuming that the “feathers” are actually feathers.”

    Little assumption needed with today’s high tech imagery. I recommend this site.

    http://www.jakobvinther.com/Front_page.html

    “And as usual, you never, for whatever reasons (fear I suspect) mention that there are other viewpoints, within evolution, concerning these discoveries.”

    None that I know of within evolutionary biology. But we have not been discussing evolution. We have been discussing whether or not Gould said that Punctuate Equilibria could be use to explain what creationists perceive as “massive gaps in the fossil record” or whether or not scientists claim that whales evolved from hippos. Neither issue is a matter of scientific/religious debate but simply a matter of record of what the scientists in question actually said in the public literature. Which is accessible for verification. On both accounts you have demonstrably failed.

    ‘I get the feeling that you personally need everything regarding evolution to be “just so”.’

    It’s true that I do keep up with the published scientific literature on a day to day basis. Can you claim the same?

    “Which is why, by the admission of quite a few evolutionists themselves, much of evolutionary theory consists of “just so” stories.”

    I think you’ll find that most scientists using such words do so in the context of showing how they themselves have tackled such a “story” and shown, via data and quantification, that we need to revise our ideas about evolutionary history. I must confess to have doing so myself a few dozen times or so in my career, although I would never have framed the traditional viewpoint in such a crass fashion.

    “Your replies are repugnant, and you impress no one but yourself (and perhaps, members of your immediate family, who, I’m sure, are kind and wonderful people).”

    My immediate family are now all dead, said to say, although I appreciate your kind views as to their nature.. But my scientific views continue to impress and inspire future generations.

    Liked by 1 person

    • as usual. confusion. Seeing as how i don’t believe there are transitional fossils, at least in the darwinian sense, i obviously see them as variations, so i don’t believe that they are transitional.
      As you make my point about feathers (i.e., sometimes their presence makes little or no difference other than decoration), it becomes clear that finding a dinosaur fossil with apparent feathers would never be a proof or indication that anything reptile to bird was going on. And for your benefit, a penguin is not a fish nor an ostrich a dinosaur. Your point?
      As for you inspiration of future generations, my we do think highly of ourselves, don’t we.

      Like

      • Chuck wrote: “Seeing as how i don’t believe there are transitional fossils, at least in the darwinian sense, i obviously see them as variations, so i don’t believe that they are transitional.”

        The personal beliefs of those outside of the science academy are irrelevant to the validity of the overwhelming evidence for the Theory of Evolution. Obviously, you have an inflated sense of your “superior” intellectual skills but I doubt that many readers are as impressed as you are.

        The tired old “creation science” trope which claims “There are zero transitional fossil forms.” wore thin long ago. ALL organisms which have reproduced are transitional—for anyone who understands how evolutionary processes operate—and the hundreds of especially significant transitional forms are well catalogued and easily found in conveniently structured lists online. Your Argument from Personal Incredulity fallacies only impress anti-evolution propagandists with similar agendas and the same old Gish-Morris-Whitcomb arguments from a half century ago. Please! Can’t you managed some new ones?

        Considering how many universities have chosen Dr. Janis’ comparative anatomy textbook to educate, challenge, and inspire their science majors, your envious whining about the undeniable respect she has earned within the international academy is just as irrelevant as your heckling of the scientific evidence for the Theory of Evolution as a surly science-illiterate bystander. Like it or not, your Kruger-Dunning protests from outside of the academy looking in, with your nose pressed enviously against the glass windows, simply do not matter to the overwhelming consilience of compelling evidence for evolutionary processes.

        If you think you have found flaws in evolutionary theory and have a better explanation for changes in allele frequencies in populations of biological organisms over time, by all means submit your research for peer review and we will be able to say that we saw history in the making. Until then, Dr. Janis has demonstrated her expertise, while you’ve just whined and boasted of your intellectual superiority. It’s boring and childish.

        Liked by 2 people

      • Christine Janis says:

        “as usual. confusion. ”

        My answer may have been a bit confused, but it’s difficult to maintain clarity when answering points like “Unless the fish immediately went airborne, joined by Rex, his dinosaur friend, —-”

        “And for your benefit, a penguin is not a fish nor an ostrich a dinosaur. Your point?”

        In a phylogenetic sense, both statements are true. But let me try a straight answer to some of your points.

        “What advantage would feathers give a creature living in the seas?”

        What sea creatures with feathers, past or present, do we know of except secondarily aquatic birds? Like penguins? But if you’re asking why fish don’t evolve feathers, that’s a fairly easy one. Feathers are epidermal structures, formed from keratin. All fish have thin epidermises, with only traces of keratin, if any. Thicker, keratin rich epidermises are a feature of amniote tetrapods, where they help to prevent water loss by evaporation. So, although fish do display a number of different skin structures, feathers would not be an option, whether advantageous or not.

        “Or a dinosaur for that matter.”

        Feathers on a dinosaur would provide the same advantages that they do in birds: insulation and display. Feathers in birds may be how they form their wing flight surface, but it’s clear not only that feathers perform other functions besides flight (or they would not be retained in flightless birds, like an ostrich), but also that feathers are not essential for flight (as they are not present in bats or pterosaurs, the other flying vertebrates). Clearly, feathers would have had to be present for other reasons before they were used for flight, as attempts to fly without any sort of wing surface would be rather futile. And the fossil record indeed shows us that feathers evolved before flight (and it’s not even clear that Archaeopteryx could fly).

        “As you make my point about feathers (i.e., sometimes their presence makes little or no difference other than decoration), it becomes clear that finding a dinosaur fossil with apparent feathers would never be a proof or indication that anything reptile to bird was going on. ”

        There are several points here:

        The dinosaur feathers are not “apparent”. They have been studied with high resolution imaging, and their identity is not in doubt. They have even been found to contain a molecular signature of beta keratin, as in bird feathers.
        Even if feathers were “just for decoration” (although decoration in birds is highly important in sexual attraction and competition), feathers are unique features seen nowhere else but in birds in the modern fauna, and in some dinosaurs amongst fossils. Thus they have been used as one of many (see below) pieces of evidence to link the two groups: what is important is their identity, not their presumed utility.
        Feathers are merely the icing on the cake in the evidence for linking birds and dinosaurs, which relies on synapomorphies (shared, derived similarities) of many features of the skull and skeleton (I could spent time listing some, but they are readily available on the internet). The similarities between birds and dinosaurs are not general “looks a bit like one” issues, but detailed features of anatomy shared between birds and dinosaurs but not seen elsewhere. (If scientists were to declare transitional forms as those that looked rather similar to each other, then they’d still be claiming that whales were fish.)
        Not only that, these unique features can be shown to be acquired in a sequence leading from dinosaurs to birds, producing a transitional series where the line between dinosaur and bird is so hard to draw that there is still debate about it. The assignation of Archaeopteryx as the “first bird” is a historical one made in the then absence of knowledge of other feathered animals. Specimens of Archaeopteryx that were discovered with only faint feather impressions, that were not spotted until later, were originally classified as dinosaurs. The skeleton of Archaeopteryx is almost identical to that of a small dinosaur —- the more avian features (fused hand bones, reduction of the tail, fusion of the sacrum to the pelvis) are not seen until the Cretaceous.

        “As for you inspiration of future generations, my we do think highly of ourselves, don’t we.”

        Let’s not forget that this was in response to this comment from you: “Your replies are repugnant, and you impress no one but yourself (and perhaps, members of your immediate family, who, I’m sure, are kind and wonderful people).” This is just one of the more recent ones — others over the past week or so include: “If humiliation is what you lust for, I would offer you more, but, as experience shows, you are capable of little more than name-calling and an incredible talent for denying anything that displeases you, though the history books may be overflowing with authentication of said topic. The unfortunate thing is that few if any of your cohorts are willing to correct you, either because they fear your insulting wrath or wish to remain blissfully, albeit mistakenly, incorrect. ”

        But as Professor Tertius has kindly explained, there is a real world basis for my statement. It is not one that I would have made without provocation, but I am entitled to self-defense amidst the onslaughts.

        Liked by 1 person

        • “It is not one that I would have made without provocation, but I am entitled to self-defense amidst the onslaughts.”

          Indeed! And even though that self-defense will make no impact upon Chuck, it will remind the honest reader of what is reality and what are Chuck’s futile attempts at fabricating a fantasy where he is a science legend in his own mind (where he imagines himself as “exposing” the errors of the science academy.)

          Many years ago I was a recurrent guest speaker at a midwestern university where the student newspaper regularly and loudly challenged the university president on every imaginable policy decision. When that president walked up to greet me at the pre-lecture reception, I asked him if that day’s newspaper headlines (which on that day had spilled into the broader newspaper and TV media nationwide) ever left him feeling exasperated and prone to fight back with all guns blazing, especially when the fact were so overwhelmingly in his favor. He looked at me and said in a delightfully droll manner, “Indiana University President Herman B. Wells** gave me some concise and wise advice when I first assumed the Presidency: ‘Never get into a urinating contest with an ant.'”

          That advice has stuck with me. It has helped me choose when to ignore the whining of anti-evidence pseudo-scholars and when to confront them.

          ** Those who saw the film about Alfred Kinsey will remember actor Oliver Platt playing the role of Herman Wells. The physical resemblance and the mannerisms were remarkably accurate. Wells is remembered for tirelessly defending academic freedom and the research interests of his faculty. (Personally, I do not believe that Kinsey’s methods necessarily always deserved the excellent defense that Wells consistently put forth, but I respected Wells for championing faculty research in a conservative state where taxpayer “revolts” often tried to curb the university’s research mission.)

          Liked by 2 people

  23. Christine Janis says:

    Chuck said “I often wonder if the cry for “better understanding of the science” isn’t actually a plea from those like you who themselves have little comprehension of their own beliefs, primarily, I imagine, because you accepted what you were taught like a two-year old accepting a spoon of mushy stuff. No real discernment, no questioning, just rote repetition of religious creed hiding in the guise of science. ”

    I think you’ll find, Chuck, that those of us who have made our mark on science have done so via questioning the current scientific paradigm and providing a (peer-reviewable and falsifiable) new approach to a particular current notion. Indeed, it would be impossible to obtain tenure at a good university without accomplishing such a feat.

    Perhaps you could enlighten us as to where and when you presented such a challenge to an accepted idea in science.

    Liked by 1 person

    • well, you know the saying,”don’t ask anyone to do something you wouldn’t do so yourself” Apparently, being world famous and all, i imagine you have at least one story if not several of changing the scientific paradigm. I would love to hear them. And i’ve heard nothing from you that differs in the least from what i’ve read from the evo community at large for the last 20 years or so. You tow the standard line. I’ve encouraged you to think outside the box, but you seem quite comfortable there. Unlike you, i don’t tend to make audacious claims as to who i am or how much people admire me or how much i inspire them. Many people found Hitler, Stalin, Castro, Napolean, etc. inspiring. I’m pretty sure i don’t. So inspiring someone does not automatically result in admirable or beneficial consequences.

      Like

      • Chuck wrote: “Many people found Hitler, Stalin, Castro, Napolean [sic], etc. inspiring. I’m pretty sure i don’t. So inspiring someone does not automatically result in admirable or beneficial consequences.”

        Godwin’s Law is rarely neglected by the evolution-denialists. Do you feel better now that Hitler has been invoked?

        Chuck, you’re embarrassing yourself. It’s painful to watch. If you insist on flailing against the expertise of real scientists, at least present some evidence-based arguments. “You tow the standard line.” is certainly true of you. It’s the same old “I refuse to accept the evidence for evolutionary processes and common descent” denialism that’s spawned thousands of articles and Youtube videos which have refuted those classic denials one by one. We’ve watched your familiar memes get regurgitated by science-illiterates for over half a century now, ever since THE GENESIS FLOOD (1962, Henry Morris & John Whitcomb Jr.) started the ball rolling for Young Earth Creationist evolution-haters and for the origins-industry entrepreneurs who’ve made many millions of dollars preying upon them.

        Please, Chuck. Something new!

        Liked by 1 person

  24. Christine Janis says:

    Chuck sad: “You seemed to have learned little from your “whippo” debacle, but denial and delusion often go hand in hand. I’ve offered to let you move on, but you insisted on being humiliated, then appeared to disappear for awhile when, on another thread, whippo became a topic of conversation.”

    I find it fascinating that, being unable to provide a single reference that supports your claim that whales descended from hippos, you still refer to it as “my humiliation”.

    Should you wonder whether or not I am conversant in the current scientific debate about the relationship between whales and hippos, my distillation of the scientific debate on the issue is a matter of public record in my contribution to the last few editions of the textbook “Vertebrate Life”.

    Liked by 1 person

    • and that, Christine, is a bold faced lie. I gave the equivalent of a page to page and a half of references, scientists names, article and magazine titles, their locations, etc. on the thread where you and i were “debating” whippo. As i suspected, you never even read them That’s one thing. No one can make you read something. It is another thing (herein referred to as “the lie”) to deny they ever existed. Unless Joel erased them (perhaps for you), they should still be there. So feel free this time to actually read and research them. I covered the different perspectives on whippo (direct descendant, close relative, distant common ancestor, along with the scientists who held such views, and the names of scientists who peer reviewed the original study). I gave you articles, page numbers, years, etc. (didn’t it strike you as strange that suddenly a thread popped up discussing it something you denied even existed?)
      This is always where you lose me Christine. I share ideas with and usually disagree with david and mega, yet we manage to keep it civil. In other words, an effort is made to remain friendly while disagreeing. There’s no braggadocio, chest-thumping, “do you know who i am”, the typical fare i receive from you. There is also a degree of humility. No one claims to be infallible, above learning something new.
      But when you outright lie, and pretend you never read something if it’s a challenge you can’t meet, that’s where and why i have lost respect for you.. I can deal with ego. I have no interest, however, in conversing with someone who ignores the difficult or denies reality. So feel free to thump your chest, regale others with your imaginary scientific exploits, and go away. i don’t tolerate liars.
      Oh, you should appreciate this. It’s not “chuck sad” (altho i am for you), but “chuck said”. If science is anything, it is precise.

      Like

      • Christine Janis says:

        “and that, Christine, is a bold faced lie. I gave the equivalent of a page to page and a half of references, scientists names, article and magazine titles, their locations, etc. on the thread where you and i were “debating” whippo. As i suspected, you never even read them”

        Chuck: I read those papers, and many more like them, long before you ever posted them. I’ve been in on the entire “whippo” debate since the 1990s. I’ve held in my hands the double-pulley astragalus of Pakicetus that convinced the paleontologists that the molecular data could not be in error, and that whales really were artiodactyls. I have written about these findings in college textbooks and edited scientific volumes. Is this “chest-thumping braggadocio”? Given the absurd accusations you’ve thrown at me for daring to disagree with you (“a disgrace to my profession” being among the mildest, comparing me to Hitler being among the most recent) my responses are simply my own version of “don’t mess with the professionals, sonny boy, we actually know the facts you are mangling in the name of free-thinking”.

        No scientific paper has ever said that whales evolved from hippos, or that there was direct ancestor-descendant relationship, as you reiterate above (although you be able to find statements to that effect in the creationist literature). And I know that because I am conversant with the scientific literature and the people who do the science (and also with the way creationists abuse science). That was the issue at stake (as documented in these posts), not whether or not scientists ever said there was a “whippomorph” relationship. And I think that that stake is now firmly through the heart of this absurd exchange.

        Liked by 1 person

Comments or Questions?

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: