Thursday, April 17, 2014

Branko Kozulic responds

Branko Kozulic has asked me to post his reply to Branko Kozulic has questions about fixation. My policy is to post letters like this without comment. We can discuss it in the comments.

I think it's an excellent example of the difficulties that many creationists will face when they try to come to grips with modern evolutionary biology.

Here's what he wants to say ...
Since Professor Moran has kindly addressed the questions I have raised, I feel obliged to respond here. But I must add that my response will be restricted to one topic only, and therefore this reply should not be construed to have the same purpose as the earlier discussion.

I find only a few minor contentious issues in Professor Moran´s post, so I prefer not to bother the readers with details about them. In my opinion, it is important that we have started to look at the core issue – the average fixation of about 100 mutations per generation, or 22,000,000 in 5,000,000 years, according to the genetic drift model - in terms of close to real-life conditions. Now we see that the simple genetic drift model needs extension, to include population splitting and recombining that leads to the postponement of fixation (I thank Professor Felsenstein for improving the clarity of this point). Furthermore, we see that in expanding populations the fixation rate is lower than the average. Thus, in today´s human population, the fixation rate per generation is close to zero. In order to compensate for the lower than the average fixation rates in some generations, it is necessary to postulate higher than the average fixation rates in other generations, if one wishes to account for the 22,000,000 fixed mutations in 5,000,000 years.

Let us consider the most dramatic case, mentioned in the comments, leading to the maximal fixation rate: the shrinking of a whole population to just a single couple, 2Ne = 2. Today we know that two unrelated human individuals differ in 1 nucleotide per about 1,000 nucleotides, so that each one of us carries about 3,000,000 SNPs. This is the maximal number (actually the maximal number is smaller because a fraction of SNPs is always in the heterozygous state) that can be fixed in this dramatic case. An interesting thing comes out to light now: the average of 100 fixed mutations per generation may result from the values that span a range of over six orders of magnitude, from less than 1, to over 1,000,000.

This raises the question of the meaning of the term “genetic drift model”. Can we maintain to be talking about the genetic drift model if the essential postulate of that model – mutation rate equals fixation rate – does not hold, because while the mutation rate changes little, the fixation rate can vary over six orders of magnitude? I think not. Drastic scenarios, known as “bottlenecks”, do not belong to the genetic drift model, in my opinion.

Now the important question is this: During the 5,000,000 years, what is the number of mutations that would have been “delayed to fix” because of the expansion of the human population, and/or due to the splitting-recombining, so that we must postulate dramatic events (“bottlenecks”) to account for their fixation? In other words, how many mutations were fixed in “bottlenecks” and how many by the ordinary course of genetic drift, in percentage? I doubt anyone can provide a verifiable answer (I kindly ask Professor Felsenstein to correct me if I am wrong). If for a “bottleneck” we take 2Ne significantly larger than 2, then many more “bottlenecks” need to be postulated in order to account for the same number of “delayed to fix” mutations. Is it possible to account for all the fixed synonymous mutations found in the human and chimp genomes by invoking fewer than two “bottlenecks” with 2Ne = 2? So that only 6 Million mutations are fixed in the “bottlenecks”, while 16 Million are fixed by genetic drift? I do not know.

And here is an additional complication. According to Wikipedia (since Professor Moran has relied on that source in his post, I follow suit):
Early humans (before Homo sapiens)

Early members of the Homo genus, i.e. Homo ergaster, Homo erectus and Homo heidelbergensis, migrated from Africa during the Early Pleistocene, possibly as a result of the operation of the Saharan pump, around 1.9 million years ago, and dispersed throughout most of the Old World, reaching as far as Southeast Asia. The date of original dispersal beyond Africa virtually coincides with the appearance of Homo ergaster in the fossil record, and the associated first emergence of full bipedalism, and about half a million years after the appearance of the Homo genus itself and the first stone tools of the Oldowan industry. Key sites for this early migration out of Africa are Riwat in Pakistan (1.9 Mya), Ubeidiya in the Levant (1.5 Mya) and Dmanisi in the Caucasus (1.7 Mya).
If correct, this information means that the time available for fixation of 22,000,000 mutations is reduced by about 2 Million years - to just about 3 Million years - because after migrating out of Africa different human sub-populations fixed different neutral mutations, due to the stochastic nature of the process. All specific human-chimp genetic differences (= all humans have them, no chimp has them, or vice versa) must have been fixed before the out of Africa migration. Is it possible to construct a genetic drift model (without “bottlenecks, with reasonable numbers) able to account for all the fixations, now within 3 Million years? I doubt it, but am willing to review a model that could dispel my doubts.

Let´s suppose that there are indeed 22 Million fixed synonymous mutations between the two genomes. I have no principal problem with that, or any other, experimentally established number. Whatever the exact number may turn out to be, scientists will continue looking for a model that fits the data best. In my opinion, no model should be rejected a priori. In order to contribute more constructively to this discussion, I ask: Why not test a model that uses 2Ne = 2 for the starting human population? With this model, for example, in the first generation 15 Million synonymous mutations might be fixed. Therefore, this model does not require multiple “bottlenecks” (perhaps just one) to account for a large fraction of the fixed mutations; while a smaller fraction - the 7 Million remaining mutations – could then be fixed in many subsequent generations in an expanding and splitting-recombining human population according to the population genetics theory.

One could argue that the starting Ne = 2 model is preferable in view of the principle known as Occham´s razor. But I would be the first one to disagree with such argumentation. Only in view of other experimental data found in the sequenced genomes one should decide which model is the preferred one; if the genome sequence data contradict one of any two models, the bad model should be rejected; and if the data contradict both, both models should be rejected.

I hope the above makes clear my thinking on this topic.


74 comments :

  1. He still seems fixated on this notion that there was a "starting human population", apparently having no clue about the continuity of descent. And hey, I wonder why he picked N=2. Shouldn't he have picked N=1 + a rib?

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    1. Beat me to it! I was going to ask if he knew their names.

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    2. Subtlety was not a strong point in Dr. Kozulic's presentation, even for me, a layperson.

      He still seems fixated on this notion

      Now John, Joe says it's not about fixation....

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  2. There's so much wrong here, but I'll stick to two points.

    1) The out of Africa migration of Homo sapiens occurred about 100Kya, maybe less. Not 2Mya. The Homo genus contained many members beyond our species, but obviously we are only concerned here with our lineage. Wiki and also the link below.

    2) There are models that examine the effective population size of humans through history. They give us very good reasons to reject a starting point of Ne=2. There is no evidence supporting such a bottleneck, and much evidence against it. See Li and Durbin 2011.

    I wrote about this back when the last ID argument for Adam and Eve came out with the Discovery Institute's Science and Human Origins. My critique of the relevant chapter is Here.

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  3. His "additional complication" is strange. Is he implying that "different human subpopulations" (presumably meaning those whose descendants still exist, since extinct ones would not complicate anything) were produced by out-of-Africa migrations 1.9 million years ago? Did he read only that particular section in the Wikipedia article and didn't have a look at the next?

    Anyway, he's a man of vesatile ignorance, from pop gen to paleoanthropology.

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    1. Piotr, you have disappointed me. No mention of numerous patents?

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    2. You are right! He's a man of versatile ignorance and numerous patents.

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    3. Sigh. Sadly, even in some academic circles, patents are treated like publications. They aren't granted in a search for "truth." They are a claim. Not necessarily a defensible claim, nor a scientifically valid claim. That a patent is granted doesn't mean the patent is defendable in court.

      Kozulic:
      https://www.google.com/?tbm=pts#q=Branko+Kozulic&start=0&tbm=pts
      if he's enforcing his patents, is a troll. Broad claims about gel electrophoresis: "2. A gel of claim 1, wherein the polysaccharide is agarose." Alone, or crosslinked by protocols going back to the 1970's.

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  4. As Prof Felsenstein might be limbering up to say again, it's not about fixation. If the reference human has 100 new mutations, and his mum and dad had 200 between them (of which 100 were passed on to him), and their mums and dads had 400 (of which 100 were passed on to him), and so on, he gets 100 new mutations for each generation you go back, so 22.4 million is 224,000 generations' worth. How long that takes depends on what the average generation length is, but 25 seem generous enough over the 5.6 million years that this would give. If people want to make it longer, they might need to up the mutation count as well, since it is age-related.

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    1. Let me just repeat, so people don't think I have changed my mind:

      Fixation is not the issue.

      Fixation is not the issue.

      Fixation is not the issue.

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    2. In the vast majority of cases where you are comparing two sequences, say yeast genes and Drosophila genes, you are only dealing with alleles that have become fixed in the population. If we were comparing human genomes and monkey genomes we could make the same assumption.

      The reason we have an approximate molecular clock in phylogenetic trees is because of a relatively constant rate of FIXATION over tens of millions of years.

      In this particular case, since the two species (humans and chimps) are only separated by five million yeas or so, some of the differences between the two reference genomes will actually be minor polymorphisms that we don't (yet) know about and haven't yet removed from the reference genome.

      Joe Felsenstein wants to emphasize that even if all those alleles are not fixed, it doesn't make any difference in the calculation.

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    3. That's not how I would read Joes comment. To me "Fixation is not the issue" reads an awful lot like "Fixation is not the issue", which means that "Fixation is not the issue".

      Under assumptions of neutrality, individual genomes accumulate mutations at a rate equal to µ and therefore you can use reference genomes with no assumptions about fixation. That fixation also occurs at µ is correct, but doesn't matter for this particular comparison.

      s=0 implies molecular clocks for comparisons between reference genomes (given constant mutation rates) and it implies a rate of fixation of µ.

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    4. @Simon Gunkel: Good points. Actually, I'd modify my statement to: "Fixation is not the issue".

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    5. Joe, please stop beating around the bush, and tell us if fixation is the issue.

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    6. Well, let's rephrase it:

      The issue is not fixation.

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    7. Or, as Master Yoda would put it, Fixation the issue is not.

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  5. Maybe I read him wrong but I thought he did not necessarily refer to an actual bottleneck of 2 people but merely as a hypothetical extreme case scenario in which it is quite easy to figure out that many alleles must at that stage be fixed; I did the same with one individual in one of the earlier threads.

    No matter at what stage modern humans left Africa (and yes, it was much later), it is still wrong to assume that nothing could have been fixed since. What the doubters here probably think about is one mutation arising in Africa in 300 BCE and then having to fixate throughout the world population a hundred years later, and that is obviously impossible. It is apparently really hard to get intuitively that many mutation being fixed worldwide in recent times will be those that have been carried around in our gene pool for tens of thousands of years, with one minority allele teetering on the edge of extinction, perhaps restricted to one family line in Asia, for the the last five hundred. It does not take much to fixate in those cases, and there will be many of them.

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  6. Say, should it not be trivial to write a simulation showing what happens with fixation rates given certain mutation rates, population sizes and expansion or contraction? Certainly somebody will have done that already? I am leaving for a short Easter holiday trip now, but if I were at work I would try to apply some Google (Scholar) to the issue.

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    1. Say, is it possible that Joe Felsenstein was at some point involved with a program that tries to estimate past population parameters given present-day genetic data?

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    2. It is possible that Mary Kuhner and Jon Yamato and others don't get as much of the credit for that program as they should.

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    3. Interesting page linked from Joe's citation: http://evolution.gs.washington.edu/lamarc/kingman.html

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    4. A little out-of-date: JFC Kingman retired in 2006 and is no longer head of the Newton Institute or Rothschild Professor. He is still the inventor/discoverer of the coalescent, however.

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  7. Branko Kozulić: it is important that we have started to look at the core issue – the average fixation of about 100 mutations per generation, or 22,000,000 in 5,000,000 years, according to the genetic drift model - in terms of close to real-life conditions.

    It isn't the core issue.

    It isn/t the core issue

    It isn't the core issue

    it is necessary to postulate higher than the average fixation rates in other generations, if one wishes to account for the 22,000,000 fixed mutations in 5,000,000 years.

    The original issue was accounting for the 22,000,000 differences between reference genomes, not accounting for that many fixations.

    Drastic scenarios, known as “bottlenecks”, do not belong to the genetic drift model, in my opinion.

    Genetic drift goes on all the time in all populations. What "the genetic drift model" means is not for me to worry about.

    Now the important question is this: During the 5,000,000 years, what is the number of mutations that would have been “delayed to fix” because of the expansion of the human population, and/or due to the splitting-recombining, so that we must postulate dramatic events (“bottlenecks”) to account for their fixation?

    We actually did not observe 22,000,000 fixations. We observed 22,000,000+ differences between the reference genomes of the two species.

    Why not test a model that uses 2Ne = 2 for the starting human population?

    Ne = 1 in that model. Which is impossible unless ribs get cloned. Why not test one that also has a Noachian bottleneck about 4,300 years ago, while the ancient Egyptians and Sumerians looked on in horror?

    Only in view of other experimental data found in the sequenced genomes one should decide which model is the preferred one;

    The 22,000,000 figure will not discriminate among all these models, just tell you about the divergence (plus coalescent) times.

    However, when you have multiple human genomes, as now people have, one can infer past population sizes. Look at this recent high-profile paper:

    http://www.nature.com/nature/journal/v475/n7357/full/nature10231.html

    (Sorry, only the abstract, with some figures as well, is in front of the firewall).

    Also, note that deciding when, in the human lineage, the species is regarded to start being Homo sapiens is another side issue, not decidable from these sequence data. Larry's original calculation was whether, with observed mutation rates and the understanding that most mutations were neutral, the difference between the two reference genomes can be accounted for, (And of course that is not an observation of whether or not the substitutions have gotten completely fixed.

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    1. Thanks, even I get it, and I'm neither a biochemist or a population geneticist.

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    2. However, I think it's true to say that most of those differences have been fixed*, since, if memory serves, two randomly chosen human genomes are something like 99.9%+ identical in pair wise sequence comparisons, ie many times more similar than a human chimp pairwise comparison.

      * Ignoring new mutations introduced in the recent human population explosion, which will have very low frequencies.

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    3. Yes, very apt comment, Nick. But my point is that we don't have to fret much about fixation to discuss the fit of theory to the similarity of the reference genomes. There can be all sorts of subtle effects of, say, population structure or temporal changes in population size, and they don't affect the observations on similarity of the reference genomes.

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    4. ... that is, the "subtle effects" are on fixatiion but doi not affect the expected difference between the reference genomes,

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    5. A copy of the Li and Durbin paper can be found here:

      http://genetics.med.harvard.edu/reich/Reich_Lab/Welcome_files/2011_Li_Nature.pdf

      (many papers, particularly the more high profile ones, can be found on google scholar via the "all x versions" option under the paper)

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  8. Why not test one that also has a Noachian bottleneck about 4,300 years ago, while the ancient Egyptians and Sumerians looked on in horror?

    Have we done the archaeology on "Holy shit! Do you know how to swim?!" hieroglyphics?

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  9. Joe,

    Since everyone, including creationists (I know that some, if not most of them, are morons...) consider you to be the expert in population genetics, I was wondering if you could suggest or design an experiment that could shed some light on whether chimps and humans are really closely related.... and diverged from common ancestor...

    As you know, I'm sceptical about this stuff.... because I have not seen any evidence... To me even you have been speculation all along... I don't buy stuff like that unless I'm presented with some evidence.... I have some funds and a lab or two where we could do some testing.... I know this is not easy.... Please let me know what would be the easiest way to prove that chimps and humans are related; have come from the same common ancestor....

    The reason why I'm sceptical is that abiogenesis was supposed to be a scientific theory, and nobody knows how it became a scientific theory... NickM and Dino-genes pretend I don't exist because they can't answer one simple question on the theme...
    So..., Joe.... What would you suggest...?

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    1. I wonder what conceivable type of evidence could possibly persuade Quest/Witton ? Maybe a Notary Public watching all the apes and hominids live and reproduce, and writing down detailed birth certificates for each individual and making them available to us?

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    2. Joe,

      As for as I know, Witton is doing time for tax evasion and more... something to do with his book and others stuff... So, unless he has access to internet in his jail cell, I can't be him...
      You.. on the other hand would rather accuse me of being someone else rather than providing some evidence.... Well... I sort of expected it because how can one provide evidence for a guess...?

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    3. I take that to be a denial that you are Witton (right?). I know nothing about any tax evasion or jail time for Witton -- just for creationist Kent Hovind. I apologize for identifying you as Witton based on highly similar comment style and comment contents.

      Now ... your answer to my question as to what evidence would convince you is ... [what?]

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    4. Evidence...? There is only one.. It can't be two....Read my comment at 5:38 PM... Let's find out if what you have been claiming here is actually supported by evidence....

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    5. Evidence...? There is only one.. It can't be two....Read my comment at 5:38 PM...

      The comment at 5:38pm was by me (wondering what conceivable evidence you would accept as really evidence). In the comment at 5:24pm by you, you did not say what that might be. I don't know what the evidence would be that would be "only one"? Fossilized birth certificates? Movies of the whole process?

      Eagerly awaiting your answer ...

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    6. As for as I know, Witton is doing time for tax evasion and more... something to do with his book and others stuff... So, unless he has access to internet in his jail cell, I can't be him...

      But if he does have access to the internet, you can? You do mention each other a lot. And your styles are both barely distinguishable from each other, and contain tics not shared by anyone else. This little mystery is much more interesting than the content of your posts. How did you find out he was in jail? There must be some public record of such things?

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    7. Yes Pest, tell us how you know that Witton is in jail for tax evasion.

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    8. Not to say fixation is the issue here, because I have it on good authority that it is not. However. Branko "Numerous Patents" Kozulic does seem to be struggling with the concept of fixation, and I wonder if part of the reason is that the does not understand how the process occurs. I don't actually see what is so "counter-intuitive" about 100 mutations becoming fixed in the human population every generation, and I wonder if Dr. Numerous Patents thinks this means something like this: Say in the current generation there is a locus which has two alleles, and each is present in about 50% of the population. Then, in the next generation, every single copy of one of those alleles is suddenly lost, and the other is instantly "fixed". And this happens with 99 other alleles at the same time.

      If Dr. Numerous Patents thinks something like this is what is being claimed, it might explain why he has trouble accepting this.

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    9. Allan Miller wrote,

      "But if he does have access to the internet, you can? You do mention each other a lot. And your styles are both barely distinguishable from each other, and contain tics not shared by anyone else. This little mystery is much more interesting than the content of your posts. How did you find out he was in jail? There must be some public record of such things?"

      Witton's genome and mine are about 92% simmilar, which could explain the observable similarities....

      Would that make me or him a common ancestor from which humans and chimps diverged...? Any thoughts on this one...?

      Joe...? Is there a flaw in the genetic testing...? How could our genomes be only 92% similar...?

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  10. Dino-genes wrote,

    "Yes Pest, tell us how you know that Witton is in jail for tax evasion."

    I will tell you how I got this info if you answer a very simple questions I have been trying to find an answer for....

    How do you get DNA without a cell membrane? And how do you get a cell membrane without a DNA..?

    I'm all ears...;) LMAO... !!!

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    1. How do you get DNA without a cell membrane? And how do you get a cell membrane without a DNA..?

      Magic. Now, about Witton and his tax affairs...

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    2. Pest, we will never respond to anything you write ever again, until you tell us about Witton in prison.


      How do you know Witton is in prison? Where did you hear it? Simple $%&#ing question.

      Of which large inmate is he the bitch?

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    3. "How do you get DNA without a cell membrane? And how do you get a cell membrane without a DNA..?"

      God did it by magic. Now answer our $%&#ing question.

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    4. It's fine to ask Quest about Whitton, but I asked him what evidence he would conceivability accept for common descent of humans and chimpanzees. He himself said that as far as evidence went "there is only one". So what could it be that Quest would find convincing? Fossilized birth certificates? Movies of the whole process?

      And all I got was ... crickets chirping. Quiet around here.

      Did he ingloriously run away? Heaven forfend! Obviously he is carefully considering his answer and will shortly enlighten us. Let's just wait for his answer .... [chirp, chirp, chirp]

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    5. I agree, it's a good question. In fact, any of the more scientifically-oriented 'Darwinism[sic]-baiters' is free to suggest a protocol whose outcome would help to settle the question for them, even in the form of a thought experiment, preferably not one involving time machines.

      I'd give Douglas Axe credit for actually attempting to address ID questions scientifically (even though he too is more in the 'Darwinism[sic] fails therefore ...' camp ).

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    6. Joe,

      I think some of my post were either removed and failed to post... I'm not going to blame Larry for something I'm not sure about... After all, he is my hero too.... :) He is probably the only high-profile agnostic professor that is at least trying or willing to see the side of ID.... I don't agree with them on many issues, so I don't think I can be labeled as one of them...ID

      Back to the issue one question at the time:

      1. Do you know or is there a way of finding out or extrapolating what the genome of an ape-like-creature was like both chimps and humans have diverged from....?

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    7. Back to the issue one question at the time:

      1. Do you know or is there a way of finding out or extrapolating what the genome of an ape-like-creature was like both chimps and humans have diverged from....?


      I thought we were first going to discuss whether humans and chimps were related. Have you conceded that and are going on from there? If you have not conceded that, we can start there.

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    8. By the way, Joe does know of a way of extrapolating the genome of an ape-like creature that both chimps and humans have diverged from. In case that provides you with a reason to concede Joe's point above.

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    9. Joe,

      Let's start with proof and theory about the ape-like common ancestor... humans and chimps have diverged from...

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    10. Joe,

      I didn't mean to put you in a position where you would have no evidence to support your beilef... Sorry about that... Just present your theory instead.... that will be fine for my students for now... I hope.....

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    11. They diverged from the human-chimp common ancestor. The question is, do you agree that there was one? We can have evidence that there was one (say, one more recent than the human/gorilla common ancestor, or the chimp/gorilla common ancestor.

      Do you understand that? Or are you under the misapprehension that we have to know what that species "was"?

      So we get back to what the evidence is that, of species A, B, and C, that (say) B and C are more closely related than A is to B, or than A is to C.

      Is there any evidence that you would find persuasive, given three species A, B, and C, that this was true? Saying we have to say what the common ancestor of B and C "was' indicates that you don't understand how arguments about common descent work.

      Sorry to put you in that position. Are you in that position?

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    12. It doesn't matter whether I agree..

      Provide evidence there was common ancestor ...

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    13. What would you accept as evidence? The kind we use to investigate common descent? You know, but showing that different parts of the genome tend to favor the same evolutionary tree.

      You do know about that, don't you?

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    14. typo, should be: ... by showing that ...

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    15. Quest thinks that, if a woman conceived a child thru artificial insemination by an anonymous sperm donor, unless she knows exactly who that donor was, the child has no male ancestor.

      Therefore God.

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    16. Joe,

      I'm willing to accept the evidence that does not require faith to believe it....

      That is why I'm trying to learn and find evidence from you...

      Just because you and Larry believe that chimp and humans' genomes are 98% "similar.... it doesn't necessarily mean that they had the same common ancestor... (I'm not even going to mention non-coding part of the genome, because I know what is going to happen....)

      A cloud and a watermelon are 98% water, but does that mean they had the same common ancestor...?

      Last time I checked the definition of evidence, it was still the same... I don't have to tell you Joe, the world's authority in genetic population acknowledged by both sides of the issue what evidence is...I feel privileged you even wanna have a discussion with me... I mean ...who am I to question you or Larry...?

      At least I'm done with Dawkins and Coyne... I'm not going to say publically what I think about those two individuals...

      What I can do... and I think I'm entitled to... is to QUESTION OR DEMAND THE TRUTH...

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    17. @Quest, the percent similarity between humans and chimps is not the issue. The question is, whether when we examine different parts of the genome, and construct an evolutionary tree from each, we tend to see the same tree instead of getting unrelated trees.

      You do understand that this is the argument, right? And if we do see evidence of this common underlying phylogeny, you do agree that this is fairly persuasive, right?

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    18. Joe, I'm 98% sure that anyone who can equate 98% similarity in DNA sequence with 98% water won't agree that anything is fairly persuasive. But good luck.

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    19. I'd love to see one of these bozos try and defend a paternity suit with their logic.

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    20. @Quest,

      Joe Felsenstein nailed it with … the percent similarity between humans and chimps is not the issue

      The issue here is one of subtlety, a subtlety that is lost on those unversed in what scientists are really talking about.

      Stop focussing on calculated similarities/differences of humans vs. chimps, but rather focus the identity and commonalities of the human/chimp similarities/differences vis–à–vis other lineages.

      Chimps and humans clearly belong to a common lineage!

      Check out this elementary introduction that can bring non-scientists up to speed before embarrassing themselves in public:

      http://www.phschool.com/atschool/phbio/active_art/cladograms/index.html

      Cladograms reveal probable relationships and degrees of relationships between groups of organisms, along with the relative times when different lines branched off (speciation occurred), showing common ancestry.

      Even my high school “Young Earth” Creationist students get it! They recognize there is a coherent and cogent story here that cannot be dismissed out of hand.

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  11. Show me a person who has never heard of a kinkajou, and I'll show you a person who wouldn't recognize a kinkajou if one was chewing on their face.
    You ask for evidence, Quest… but it's far from clear that you'd recognize any such evidence if you saw it. Felsenstein is right to ask you what you, Quest, would accept as evidence for the notion that chimps and humans share a common ancestor. Your refusal to answer Felsenstein's question is persuasive evidence that you're Yet Another Goddamn Creationist who doesn't know jack about evolution, but nevertheless knows that evolution must be wrong.

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  12. I am not certain how gladly recieved these series of posts will be - but here goes:

    Misconception 1: Darwin formulated the Theory of Evolution.

    Correction: Darwin did describe two mechanisms by which evolution can occur. These theories are called the Theory of Natural Selection and Sexual Selection. There are other mechanisms as well.

    Misconception 2: Evolution contradicts the Bible. Christians cannot believe in Evolution.

    Correction: This is a minority Christian view. First of all, there are many contradictory and contending versions of Christian Creationism that can be summarized under the two competing categories of “Young Earth” vs. “Old Earth”. Adherents to one or other version of Creationism include; Assemblies of God, the Evangelical Presbyterian Church, the Free Methodist Church, Jehovah's Witnesses, the Missouri and Wisconsin Lutheran Synods, Pentecostal Churches (including Pentecostal Oneness churches), Seventh-day Adventist Churches, the Christian Reformed Church and the Southern Baptist Convention.

    Catholic and Orthodox Christians endorse evolution; together with all mainline Protestant denominations; including as well a variety of different Baptist and Lutheran churches. Bottom line: the majority of Christians do not believe that Evolution contradicts the Bible.

    Misconception 3: Any reading of the Book of Genesis necessarily contradicts Evolution!

    Correction: Only a bizarre and literal interpretation of the Bible contradicts Evolution. Any such literal interpretation of Genesis would compel astronauts to wear scuba-gear and water-wings. According to the Book of Genesis, the world is flat and the center of the universe; the moon, sun and stars are embedded in a crystalline firmament, beyond which exists primordial water. In other words, outer space is full of water. It gets better: when God opened the windows of this firmament, all that celestial water rushed in causing Noah’s flood.

    Let us examine how the Book of Genesis starts: "In the beginning” (Heb. בְּרֵאשִית בָּרָא). Remarkably, Genesis does not start with “בָּרִאשׁוֹנָה” as is employed so frequently in the Hebrew Testament elsewhere. Clearly Genesis did not intend to teach the sequence of the Creation. The structure and vowelization of the Genesis’ בָּרָא is quite peculiar. Much commentary has been written on this one expression prompting exhaustive midrashic clarification. Since time immemorial, Jewish sages (including Akiva and Rashi) understood the literal sequence of the Creation (as written in Genesis) to be impossible. In other words, a proper appreciation of the original Biblical Hebrew obliges an appreciation that the Pentateuch (the first five books of the Bible) cannot blindly be read in a mindless and literal manner. Ultra-orthodox rabbis including Chassids all agree on this point.

    Misconception 4: There is no evidence to support evolution and the theory of natural selection

    Correction: There are ‘tons’ of evidence from fields as diverse as zoology, botany, genetics, molecular biology, biochemistry, paleontology, geology, physics, cosmology, archaeology, prehistory and history.

    Misconception 5: Belief in Evolution is just as much “belief-driven” and “faith-based” as Christian embrace of scripture.

    Correction: "Science is the systematic enterprise of gathering knowledge about the world and organizing and condensing that knowledge into testable laws and theories" E. O. Wilson in Consilience.

    “In so far as a scientific statement speaks about [scientific] reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about [scientific] reality.” Karl Popper

    By restricting themselves to the empirical method, scientists restrict their endeavors to what can be directly measured and observed in the natural world. Nothing in the empirical method requires an act of faith or suspension of belief. Science by its very nature remains undeniably testable, measurable and objective.

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    1. Misconception 6: Empirical Science is hostile to faith and religion. Science cannot respect religion. Science leads to atheism.

      Correction: Not at all! As far as the existence of God or any other religious belief is concerned – science is neutral. As a matter of fact, many scientists are devoutly religious. It is true that the empirical point of view is very restricted, which would explain why everyone (scientists included) also have a variety of non-empirical beliefs. Let us presume all scientists are enlightened and believe in the inherent and equal worth of all individuals. How can such an idea be dissected or placed under a microscope to be studied by the empirical method? Granted, a Creationist may have a slightly larger repertoire of non-empirical beliefs than some scientists. However, all scientists are constrained to respect any such non-empirical thinking given the very existence of scientists’ own non-empirical repertoire of beliefs; especially when considering commonalities based on identically enlightened premises.

      Misconception 7: There are many scientists who do not support the theory of evolution.

      Correction: Scientists may disagree which mechanism is most important and when; but, support for evolution and natural selection is constant. There is no such thing as a bona fide Biologist who denies evolution. There are a few misguided and confused individuals with Biology PhDs who embrace “Creation Science”. There also exist some bona fide scientists (specialists in other fields) with little or no expertise in Biology who remain unclear on evolution. However, no bona fide peer-reviewed scientists publish any version of Creationism in professional scientific journals. That is a very important distinction.

      Misconception 8: Evolution is only a theory and that means it is only a guess.

      Correction: Evolution is fact and theory. The only facts in science are data points. Scientists use the term “theory” differently than laypeople. In science, “theory” does not imply “imperfect truth” or some sort of guess. In science, Theories are as good as it gets; better even than Scientific Laws. Scientific Laws can be contradicted (ex. There exist many contradictions to Mendel’s Genetic Laws). Other scientific theories include cell theory, atomic theory, and the germ theory of disease. The notion that the Earth goes around the Sun (and not vice versa) is also theory, no different than Evolution. “Truth” is the purvey of epistemology and theology; whereas “theory” is as good as it gets in science!

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    2. Misconception 9: “Creation Science” or” Intelligent Design” are cogent alternative scientific theories to Evolution.
      Correction: By definition, the supernatural cannot be measured or observed by science. By definition, “Creation Science” or “Intelligent Design” invoke the supernatural. Therefore, neither is measurable, testable, empirical or scientific.

      The empirical method is testable and therefore scientific. Let us discuss the empirical method. Observations are made, data is collected and laws are made. Laws are simply generalized descriptions of observations. Scientists then construct predictive models to better explain their Laws. In short, scientific laws explain what is happening; theories describe how or why things happen.

      Remember that in science, theories are as good as it gets and remember that different theories can co-exist. Darwin was the first to recognize that the Theory of Natural Selection could co-exist with the Theory of Natural Selection.

      As important as Johannes Kepler's Laws of Planetary Motion were; Kepler nonetheless provided no empirical model or explanation why planets moved as they did. Instead, Kepler suggested that planets were being pushed along their orbits by angels. OK, Kepler’s laws were empirical. But because Kepler's theory invoked the supernatural, his theory was ipso facto non-empirical.

      Later on, Newton came up with his law of universal gravitation (a more general and inclusive summary of Kepler’s Laws) and then proposed a theory that proposed gravity was some emergent property of matter. Newton’s laws and theory were excellent approximations of the effects of gravity on a small or local scale. On a cosmological scale, Newtonian law and theory both break down. Einstein accounted for the new data with his theories of Relativity. Relativity Theory is only required when there is a need for extreme precision (such as describing Mercury’s orbit) and when dealing with extremely massive and dense objects (such as stars).

      Einstein came up with a different Theory of Gravity, proposing gravity was in fact a property of the curvature of space-time. Newton’s theories allow us to keep our satellites in synchronous orbit around our planet. Einstein’s theories allow us to synchronize satellite’ clocks with our clocks back on Earth. As even more data was collected at both the quantum level and cosmological levels, Stephen Hawking and Roger Penrose supplemented Newton’s and Einstein’s theories with a yet another and even more modern theory of gravity – and so the story continues!

      Nobody ever dared suggest that Gravity was untrue, even as new theory superseded old theory. Gravity is fact as well as theory. Similarly, Evolution is also fact and theory. Theories of Evolution and Gravity are both empirical and by definition are not based on faith or supernatural intervention. The champions of “Creation Science” or “Intelligent Design” invoke divine intercession and are no different than Johannes Kepler who invoked the existence of those very patient and obliging angels charged with the unenviable task of pushing planets along their orbits.

      Misconception 10: The interconnected and intricate beauty of the human body could only be explained by “intelligent design”.

      Correction: As a matter of fact, the design of the human body is very unintelligent and very jerry-rigged. Sinus infections occur with unnecessary frequency because our sinuses are still “designed” to drain when we are in the horizontal position, as were once our evolutionary ancestors. Hemorrhoids, inguinal hernias and herniated vertebral discs are all a consequence of what amounts to poor structure design of our bipedal species but perfectly understandable in the light of evolution, when presuming a quadrupedal ancestor. Many other examples could be cited; check out the writings of Stephan J. Gould or Neil Shubin.

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    3. Misconception 11: Evolution contradicts the Second Law of Thermodynamics. Entropy contradicts Evolution. The complicated intricacy of life forms could not be getting more complicated i.e. more ordered as time progresses.

      Correction: A naïve misunderstanding of the second law of thermodynamics suggests that any and all systems in the universe get more disordered and random as time goes on. There is nothing about the second law that prevents one part of a closed system from getting more ordered, as long as another part of that same system is getting more disordered. But what exactly is meant by disorder? Let us examine the thermonuclear reactions of stars. The intricate complexity of the entire periodic table of elements is being generated as time progresses; starting with the simple fusion of Hydrogen atoms. Atomic Evolution is no different than Biological Evolution from a thermodynamic point of view; viz. complexity increases with time.

      Misconception 12: Evolution is “Survival of the strongest”. The strongest wins…

      Correction: Survival of the fittest. Fittest refers to reproductive success. Whoever makes the most babies wins…

      Misconception 13: Evolution is directional or has a goal. It leads to perfection.

      Correction: Evolution is the result of random mutations and as a process can select for the organisms best adapted to their current environment. Modern humans are no more “evolved” than modern chimpanzees.

      Misconception 14: Individual organisms evolve.

      Correction: Individuals cannot change their genetic make-up; only populations can change allelic/gene frequency.

      Misconception 15: Evolution does not take very long.

      Correction: Evolutions is ongoing – it has been happening for as long as life has been on this planet. Mind you, punctuated equilibrium as a phenomenon has also been suggested.

      Misconception 16: Evolution stopped a long time ago.

      Correction: Changes in the frequency of alleles in populations are continually happening – evolution is still happening. Taking the flu shot constitutes tacit admission that evolution must be true.

      Misconception 17: Evolution implies that apes evolved into humans; in other words, today’s species are derived from present-day organisms.

      Correction: Apes and humans share common ancestor several million years ago. There is a big difference! Anybody who persists in citing “the croco-duck” fallacy is being intellectually dishonest. Similarly; any spurious straw-man argument that Chimpanzees evolved into humans is simultaneously disingenuous and insulting to Chimpanzee-kind. (… with a tip of the hat to Thomas Henry Huxley)

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    4. This deerves its own post:

      Misconception 18: Recent DNA sequencing evidence establishes that human and chimpanzee DNA identity is far less than 99%. This new evidence supports the Creationist contention that chimpanzees and humans could not have evolved from a common ancestor.

      Correction: When comparing human Chimpanzee DNA similarities, the old fashioned interspecies DNA hybridization- hydroxyapatite assays underestimated the insertion-deletion differences (“indels”) that could only be determined by direct computer comparison of chimpanzee human sequences. There may be merely 35 million nucleotide differences, but there are also 5 million “indels” and even chromosomal rearrangements to take into account. Depending on how these later categories are counted as "DNA differences" would add around another 3% to 4% to the total DNA differences between humans and chimpanzees.

      The fact remains – humans and chimps are still more closely related to each other than horses are to donkeys!
      The new data actually supports evolutionary theory by with the so-called "less is more" hypothesis. A relatively minor number of "genetic events" (viz. those “indels”) can actually result in dramatic global changes in gene expression together with dramatic morphological and behavioural changes; and all with a relatively small number of genetic “indel” events. Niles Eldredge and Stephen Jay Gould proposed the fossil record could be best explained by “Punctuated Equilibrium” where evolutionary change was rapid and drastic. These “indels” could provide just such a mechanism for “Punctuated Equilibrium”.

      Furthermore, human – chimpanzee differences may be no greater than differences already existing between sub-populations or sub-species of chimpanzees. That sequencing still remains to be done. Barbara McClintock taught us that the genome is always in dynamic flux and not at all static, we should remember her insightful contributions when attempting to understand evolution.

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    5. Misconception 19: Mules and hinnies are infertile and represent evolutionary “dead-ends”. This proves chromosomal rearrangements cannot provide a mechanism of reproductive isolation and speciation.

      Correction: Such reasoning puts the evolutionary cart before the horse (pun intended). Simply put, an ancestral population A can generate a different population B by some chromosomal rearrangement (or “indel”) event. These two populations can still interbreed, albeit with reduced fertility. Population B can also generate a different population C by yet a different chromosomal rearrangement (or another indel event). These two populations can also interbreed, albeit again with reduced fertility. However, Population A and Population C cannot interbreed!

      That means, reproductive isolation can occur before lineages diverge by adaptive radiation. For example, the karyotype of the domestic horse (2n = 64) differs from that of Przewalski's horse (2n = 66) by an extra chromosome pair either because of the fission of domestic horse chromosome 5 in Przewalski's horse or the fusion of Przewalski's horse chromosomes 23 and 24 in the domestic horse.

      This is the clincher! Przewalski's Wild Horse and the domesticated horse (despite their karyotype differences) can be crossed to produce fertile offspring, with varying karyotypes.

      Misconception 20: Speciation via reproductive isolation is a priori impossible. If the first individual in a new lineage is reproductively isolated from the original population, with whom would this individual mate to establish a new lineage?

      Correction: Any reproductively isolated individual at the beginning of a new lineage could always interbreed with siblings who shared identical chromosomal rearrangement or indel events. Such inbreeding would establish a new population leading eventually to a new species. That is what scientists think may have happened with humans. All 7 billion humans have a very limited level of genetic diversity; merely on the order of a somewhat large chimpanzee population. Genetically, humans resemble an inbred subset of the chimpanzees.

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    6. Misconception 21: Evolutionary Science would have us believe that Ontogeny recapitulates Phylogeny, in other words, human embryos at some point have yolk sacs and gills.

      Correction: Not at all. Comparative Embryology reveals similar stages in development (ontogeny) among related species. These similarities do help establish evolutionary relationships (phylogeny), but embryonic development does not recapitulate or replay evolutionary history.

      Why do we imagine human embryos have structures that resemble gills slits, tails and yolk sacs? That is because our ancestors’ embryos had similar embryonic structures that immediately developed into gills slits, tails and yolk sacs! However, small and subtle changes in embryogenesis lead to profound evolutionary change!

      For example, human embryos have pharyngeal slits and pharyngeal arches which resemble the embryonic pharyngeal slits and pharyngeal arches in fish embryos. However, neither human embryos nor fish embryos have gills per se. Those pharyngeal slits and pharyngeal arches develop into different structures in different animals, that much is clear.

      Evolution merely claims that these common embryonic stages represent the basic vertebrate embryonic body plan of the common ancestor of all vertebrates which still remain the same starting points for all descendent embryos! The fact that mammal embryos must undergo incredibly convoluted and illogical developmental pathways is testament to their evolutionary heritage. Meanwhile, the fossil record confirms the intermediate/transitional evolutionary stages for these structures as they evolved to assume different functions.

      Misconception 22: The missing link for apes and humans has never been discovered, so evolution remains unproven.

      Correction: There are a number of problems with this attempted rebuttal. First of all there is no such thing as a single missing link. Humans can trace their ancestry back to a great number of ancestral forms. Chimpanzees can do the same. In other words, there are many links, not just one.

      This misconception could be construed differently. Perhaps the fossil for the last (most recent) common ancestor of both humans and chimpanzees lineages has not yet been discovered. That is debatable in light of the recent “Ardi” discovery. In any case, the argument is still not valid. Absence of evidence does not constitute evidence of absence!

      That said, the common ancestry of many other disparate and divergent lineages has been well established including those lineages belonging to horses, whales and plants. For the record, horses and whales are “cousins” in evolutionary terms, as they have a relatively recent common ancestor. The reality of Evolution is indisputable, both as fact and as theory.


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  13. Over the years, I have tallied a list of common misconceptions uttered by my students. Remarks such as if Chimpanzees evolved into Humans, why are there still Chimpanzees… etc

    And over the years, I have attempted to compile a list of responses to such common misconceptions that adhered to my professional code of conduct, I am not permitted to belittle or disparage religious belief.

    I am not certain exactly who will take greater umbrage at my list – Larry and his supporters or Branko and his acolytes.

    My intent was to bring so-called Intelligent Designers aka Creationists-lite up to speed on certain questions and avoid unnecessary palaver.

    I reckoned if Intelligent Designers aka Creationists-lite could master the answers provided to these misconceptions, we could spare much band-width and waste much less time.

    My answers were not designed to be the final definitive responses to these questions, but rather a gentle point of entry for Intelligent Designers. A foundation that could be built upon as it were. Don’t forget this list was complied with high school students in mind.

    There I hope Larry feels better now…

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  14. Upon reflection and harking back to lessons learned on this forum - I need to revisit Misconception 13: Evolution is directional or has a goal. It leads to perfection.

    Correction to my Correction: Evolution can be the result of random mutations, grist for selection generating the organisms better adapted to their current environment.

    However, modern humans are no 'more evolved” than modern chimpanzees or intestinal parasites.

    That all said - random Genetic Drift is probably the major driver of evolution and most evolution is neutral.

    I am in debt to those patient teachers who take the time and effort to correct my naïveté

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    1. In biology, successful designs remain in the biosphere’s interconnected collective (RNA/DNA) memory to help keep going the billions year old cycle of life. We are the result of a molecular learning process that keeps itself going through time by replicating previous contents of genetic memory along with good (better than random) guesses what may work better in the next replication, for our children. The resulting cladogram shows a progression of adapting designs evidenced by the fossil record where never once was there not a predecessor of similar design (which can at times lead to entirely new function) present in memory for the descendant design to have come from.

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