An Anti-Darwin moment (one nut, two hammers)

While travelling, I stumbled across the following Tweets:

James Plaskett @JamesPlaskett 19 Jun
@Dragonblaze @LogicalNarwhal Oh dear, O Lor…´genetic evidence´´ That´s not too specific, is it? What about cytochrome c

James Plaskett @JamesPlaskett 19 Jun
@Dragonblaze @LogicalNarwhal Shame re Youtube Here´s just one exposition against cytochrome c similarities existing –

Just out of curiosity, I took a look at this video, which I invite you to do.

I’m taking a guess that the presenter (Jay Wile) has been looking at the data from a paper rather like Dayhoff et.al.(1973). That paper is online here:
http://www.staff.ncl.ac.uk/alan.ward/Phylogenetics/Resources/Dayhoff_cytc_1973.pdf …and the key figure is attached to this post.

The chart is the simplest consistent family tree, and the figures on the chart are a sort of ‘evolutionary distance’, representing the proportion of amino acids that are different from a hypothetical shared ancestor.

The various amino acid sequences used are not all given in their entirety by the Dayhoff paper, but a reasonable selection is given online as a class exercise by the University of Indiana: http://www.indiana.edu/~ensiweb/lessons/molb.aa.pdf

Comments:

1. I don’t think you have to be very selective at all to get the percentages quoted, and neither do you have to lie. (‘Liar’ is a pretty
serious accusation where I come from, and if you’re going to throw it around, you’d better have some bloody good evidence that a lie has been
told.) The evidence says ‘I’m a tree!’ about as clearly as it can, and that’s all I would expect it to do.

2. The prediction of evolutionary theory is not that the horse sequence will be the most different from the bacteria of the six, as Wile suggests. The prediction of evolutionary theory is that the longer a group has split off from a common ancestor, the more sequence differences will accumulate. The data bear this out exactly. I also imagine that is roughly the tree you would draw after looking at photographs/micrographs of these species, knowing nothing of cytochrome c.

3. I think what Wile has done to get his pink line is added up the total distances on the chart of various species from the bacterium and queued up the results. What he has discovered is, the bacterium is the most distant relative of all the others, and the yeast most distant of the others from the bacterium. The slope is shallow, because he is measuring from a distant point among a set of twigs, all of which are on a different branch. (Now, that *is* being very selective.) Also, Wile is suggesting that there is some significance to the fungus (yeast) being further away from the bacterium on that tree than are the mammals, but there is not.

4. I was really struck by this video because I excpected something better. Plaskett is not an unintelligent man: he is former British Chess
Champion and sometime winner of Who wants to be a Millionnaire? He seems to have some bee in his bonnet about Darwin, enough to want to label himself with “Anti-Darwinian” in his Twitter profile, and is presumably at ease with attracting attention by this label, and well-rehearsed in dealing with that attention… yet this dismal video is what he wanted to steer the conversation toward, as the Tweets show.

______________________________________

(tl;dr) version:
[My first rant just kept on growing]

In these exchanges, I decided to get involved:

Dave Regis @DrDaveExeter 21 Jun
@JamesPlaskett @Dragonblaze @LogicalNarwhal any better explanation than evolution of cytochrome c data http://www.indiana.edu/~ensiweb/lessons/molb.aa.pdf ?

James Plaskett @JamesPlaskett 22 Jun
@DrDaveExeter @Dragonblaze @LogicalNarwhal There are loads on Youtube. ALL genetic evidence Chromosme 2, Inserted viruses, etc counterable.

Dave Regis @DrDaveExeter 22 Jun
@JamesPlaskett @Dragonblaze @LogicalNarwhal Agree there are loads of videos on YouTube. To be more specific: can you see how Jay Wile …

Dave Regis @DrDaveExeter 22 Jun
@JamesPlaskett @Dragonblaze @LogicalNarwhal …does not challenge explanatory power of evolution for the sequences of cytochrome c I linked?

Answer came there none.

Just to take a hammer to this particular nut, then:

The video linked is called “What Does the Cytochrome C Prove? Not Much”
and is an extract from a longer talk by one Jay Wile.

Let’s look at the evolutionary argument:

1. Evolution by natural selection (Darwin’s idea) will result in a
branching tree of life, with descent of perhaps many varied groups from
a common ancestor. There is a famous sketch by Darwin of this idea in a
notebook:
http://www.nhm.ac.uk/resources-rx/images/1008/darwin-i-think-43863-1.jpg

2. Cytochrome c is a protein, made up of a chain of over 100 amino
acids. It’s found in all cells, and does the same job in all cells,
being part of the apparatus that releases usable chemical energy from
food. It’s found in the cell plasma of bacterial cells and in the
mitochondria of ‘eukaryote’ cells (everything but bacteria).

3. The chain of amino acids can be ‘sequenced’ and we find different
amino acids in the cytochrome c from different organisms. It’s not
random. Some positions in the sequence are strongly conserved, and are
the same in all organisms for which I have found data. But some amino
acid positions are occupied by different amino acids in different
organisms, and more physically similar organisms have more similar amino
acid sequences.

4. The simplest explanation of this pattern is to say that the sequences
represent a family tree from a common ancestor, where the sequence of
amino acids can wander away from the original common sequence, and the
longer ago that two branches of the tree diverged, the more their
sequences will have diverged too. It’s thought that these changes are
mostly irrelevant to the functioning of the molecule and are mostly
random in their origin and spread. They accumulate over time, and so the
longer ago the tree branched, then the more changes accumulate.

5. The tree suggested by molecular evidence is exactly the same tree as
you might have suggested by looking at the anatomy or physiology of the
species (monkey closest to human).

OK, let’s look at the video:
http://www.youtube.com/watch?v=cDBQz_Mq5ps

The argument here seems to be:

(1) The evidence about cytochrome c is widely quoted in biology textbooks
in the following form, showing percentages of similarity to human
cytochrome c of the sequences of different organisms, and that this
shows the relatedness we might expect among eight organisms:

1% Rhesus Monkey
8% Rabbit
12% Horse
21% Tuna
28% Screwworm
38% Wheat
47% Yeast
62% Bacterium

(2) However, “evolutionists lie about it” and “you have to cherry-pick
to get this trend” (i.e. be unfairly selective).

(3) This is because you would expect from evolutionary theory that the
simplest organism (bacterium) would be the most different from the horse
of the list of organisms (maybe just Wile’s list of 5).

(4) However, the actual sequence of difference is shallow in its slope
and slopes in the wrong direction:

“If I were to take a bacterium and look at its cytochrome c and compare
how different it is with these creatures’ cytochrome c I would expect
the line to look like this… until the horse is the most different.
What do the data say? In fact… the yeast is actually a little less
similar to the bacterium than the horse is to the bacterium… but the
pink line shows very little trend.”

OK, how does this stack up against the evidence? At Indiana, they’ve set
the examination of the cytochrome c evidence as a class exercise, so you
can see it for yourself:

http://www.indiana.edu/~ensiweb/lessons/molb.aa.pdf

As far as I can see:

1. Those widely quoted percentages look about right.
I make them:
2% Rhesus Monkey
9% Rabbit
12% Horse
20% Tuna
25% Screwworm
38% Wheat
41% Yeast

I have even shown my working (cytcaa):

There isn’t a bacterium in the Indiana data set, but I’m satisfied that
the percentages quoted by Wile are correct. But note: I’m not selecting
among the amino acids of cytochrome c, I’m using the whole sequence
given. Also note: the data from other available species show exactly
what you’d expect, in that birds are closer than fish but further away
than non-human mammals, and reptiles are closer than fish. [I think the
Indiana data set has been simplified a bit, compared with the
original data I can find, but not by much (112 positions given out of a
possible 125).] No cherry-picking here!

2. Hmm, I’m not fond of the accusation of lying. Evolutionists and
anti-evolutionists may be mistaken, but to be accused of deliberately
making false statements is quite a thing. The nature of the lie is not
explicitly stated by Wile, but as far as I can tell the percentages are
correct and the data has neither been unfairly selected among the
amino-acid positions nor among the available species to show a
predetermined result.

3. The prediction given by Wile as derived from evolutionary theory is
not as Wile gives it. A prediction is best put something like I did
above: organisms sharing a recent common ancestor will have protein
sequences more similar to each other’s than to those of organisms whose
most recent common ancestor was longer ago, so we might be able to
reconstruct a ‘family tree’ of organisms using such sequences. (For a
very clear list of the actual predictions of evolutionary theory and how
they stack up against the available evidence, see
http://www.talkorigins.org/faqs/comdesc/section4.html .)

The ordering of differences from the bacterium first can’t be done
using the information in the Indiana set, which doesn’t include a
bacterium. A bacterial sequence is included in this 1973 paper, though,
which uses more organisms and uses more positions in the sequence:

http://www.staff.ncl.ac.uk/alan.ward/Phylogenetics/Resources/Dayhoff_cytc_1973.pdf

The simplest consistent tree has been constructed and is shown on p.105
of the paper.

It’s much as you might expect from examining the physiology, anatomy,
and other characteristics of the organisms. I think that in order to
construct Wile’s reversed, shallow slope – and I’m making a guess here –
Wile has done something like measure the distance from the bacterium
along the various branches of the Dayhoff tree. Wile is suggesting that
there is some significance to the fungi being further away from the
bacterium on that tree than are the mammals, but there is not. The evidence
says ‘I’m a tree!’ about as clearly as it can, and that’s all I would expect it to do.

Measuring distances from the bacterium (instead of the human or horse)
is itself being very selective. The slope among the mammals may indeed
be shallow, but that’s because you’re measuring from a distant point
among a set of twigs, all of which are on the same branch. The distance
from the bacterium is not revealing of anything very much, except that
the common ancestor of the bacterium and the eukaryotes was a very long
while ago. Wile is claiming that a prediction that evolution does not
make is not borne out by these results. All that is actually happening
is that yeast has been diverging from its common ancestor with bacteria
for quite a while (with its short life cycle), and the fact that it now
has the most different sequence to the bacterial one comes as no
challenge to evolutionary theory.

This is all pretty ancient stuff now. The molecular evidence accumulated
since the 1970s is absolutely overwhelming, and has resulted in a single
highly consistent tree, where you do end up with the order of
relatedness to humans as given in all the books, using a variety of
different molecules. For example, a giant sequencing project using
ribosomal RNA resulted in this magnificent series of results and images:
http://www.zo.utexas.edu/faculty/antisense/downloadfilestol.html

And if you have some patience, you can still pick out a sequence of
declining closeness to humans:
Rhesus Monkey
Rabbit
Horse
Tuna
Screwworm
Wheat
Yeast
“Bacterium”

(Our view of what a bacterium is has itself evolved since 1973. There
seem to be two major groups, not very closely related to us or each
other.)

I simply cannot find the other “99%” of contradictory evidence that Wile
talks about and cannot imagine what it is, if it is anything at all. At
one point he says that you have to be very selective in which species
you choose to get the percentages to line up as they do, but the Dayhoff
paper was clearly doing its best in 1973 to use much (or all) of what
was available then, the list given by Indiana now seems to be a fair
cross-section across groups, and the 2006 rRNA sample is about as
comprehensive as you could hope for.

So, I don’t think Wile can justly conclude what he does, and therefore
that video clip doesn’t really do the job Plaskett thinks it does. Maybe
there are better arguments against Darwinian evolution, but remember
this was Plaskett’s chosen topic, so presumably one of his
stronger objections, and I would hope that he chose a bit of video which
he had seen before and had confidence in.

And not just Plaskett thinks the cytochrome c evidence is bogus; here’s
a quote from Kent Hovind, a prominent creationist, which I found while looking for the other “99%”:
“Well, now, hold it. If you want to just pick one item and that’s supposed to prove relationship, did you know that human Cytochrom [sic] C is closest to a sunflower?”
http://www.christianforums.com/t12710/

I think a glance at the data shows that to be utterly false. The human
sequence might be closest to a plant sequence if the choice is among
(1) plant, (2) protozoan, (3) bacterium, but if the choice is the original
list of eight organisms, it really isn’t.

Reflections:

1. I was really struck by this exchange because Plaskett is not an
unintelligent man: he is former British Chess Champion and sometime
winner of Who wants to be a Millionnaire? He seems to have some bee in
his bonnet about Darwin, though, enough to want to label himself with
“Anti-Darwinian” in his Twitter profile, and presumably at ease with
attracting attention by it… Yet cytochrome c is what he wanted to talk about, presumably
because he thought it was one of the weaker points in the neo-Darwinian edifice.

2. What on earth made Plaskett think that video would do?
I guess we all have to take some things on trust; did Plaskett trust
Wile to be treating the evidence fairly, because he has a PhD? Oh, if
only the world worked like that. If someone is flying in the face of
99+% of hard-won scientific opinion, they might be a misunderstood
genius, but more like they might just be misinterpreting and even
misrepresenting the evidence (deliberately or otherwise), being unable
to accept evolution for religious or other a priori reasons.

3. One commenter dismissed Plaskett’s suggestions on YouTube with request for
‘peer-reviewed papers only’, which would surely be welcome if available,
but I’m happy to take the argument on Plaskett’s terms, and use the
video he wanted to use. We find that the cytochrome c evidence shows
what evolutionary science would expect it to show. And neither alternative
explanations for the data, nor disconfirming evidence, are to be found.

4. Plaskett does not to offer an alternative explanation for the data
himself, and perhaps feels under no obligation to do so. As regards
alternative explanations and their evidence, Stephen Law is very good on
this:
http://stephenlaw.blogspot.co.uk/2013/05/correction-to-believing-bullshit-chpt-2.html

His point is that modern evolutionary theory makes some big commitments
to predicting how the world ought to look if Darwinian evolution is
true, and is and should be given much credit for getting it right. So,
if the human sequence were closer to the rabbit’s than the monkey’s, or closer to the
bacterium’s than the fish’s, then evolution would be busted as an
explanation for those results. I don’t know what predictions a
creationist like Hovind or Ham would make about the fossil record, about
amino acid sequences, or anything else in biology, but until they put
their predictions where there mouths are, they’re not really in the
game.

D

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7 Comments

Filed under science & natural history

7 responses to “An Anti-Darwin moment (one nut, two hammers)

  1. First of all, and to correct what you have blogged, I do not think the cytochrome c comparison evidence to be anything like one of the strongest points against neo-Darwinism and have recently said as much on Twitter.
    I addressed it there because someone had challenged me about it.

    I do call myself ´anti-Darwinian´ in my Twitter profile, but add that I am also ´not too arsed what gets people harmlessly through their lives.´

    The Dennetts, Dawkinses, Joneses and Regises of this world strike me as unlikely to be steering aircraft into buildings nor shooting people dead in churches for having performed abortions. So I regard their and your confidence in the theory as, at worst, clinging on to an outmoded Victorian creation myth.

    This guy @richardmilton (on Twitter), is a friend and the best summary of arguments against neo-Darwinian theory is in his book, Shattering The Myths of Darwinism –
    http://web.archive.org/web/20041010012504/http://www.alternativescience.com/shattering-the-myths-of-darwinism

    If you have not already read it, may I recommend it?
    Milton has no religious beliefs “… and am not interested in such questions, but greatly value my independence of thought”.
    Here´s Richard, interviewed by an odd gang, further outlining his problems with modern evolutionary theory –

    Michael Denton´s Evolution: A Theory In Crisis was also a seminal influence on me.

    Here´s a few brief points made by him on why he came to disbelieve in Darwinism.
    Unfortunately, it´s a clip from a Creationist video –

    And this guy- http://www.youtube.com/watch?v=k5r5cRlctLM
    in the 3 Youtube presentations there, speaks for a lot of us.

    He´s much liked by the Discovery Institute, although he too claims to have no religious beliefs.

    The immediate problems that I always had with the idea, from a very young age, were
    a) the improbability of evolution proceeding along those lines and
    b) the irrelevance of ´survival of the fittest´ as an explanation for the way some things make a living.
    I mean, re that last point, it´s all very well for you to tout amino acid sequences as evidence for common descent.
    But how does Darwinian thinking sit with creatures which have complex life cycles and/or undergo metamorphosis?
    e.g a caterpillar?

    As far as I´m concerned a butterfly refutes modern evolutionary theory.
    No further evidence required.

    Or the doppelgangers of Australia where, with the exception of the reproductive systems, we have exactly the same animals in terms of wolves, rats, etc which have come about, the leading Darwinists of the 20th century assured us, through nothing more than adaptation and natural selection.
    They also, quite by themselves, refute modern evolutionary theory.
    No further evidence required.

    Those two still remain perhaps the biggest problems for me when asked to accept a theory of gradual change.

    But when I began to read non-religious critics such as Macbeth, Rattray-Taylor, Koestler, Denton and Milton I saw that there were many, many others.

    I have touched upon some at my blog –
    http://james-plasketts-coincidence-diary.blogspot.com.es/search?q=lyall+watson

    and

    http://james-plasketts-coincidence-diary.blogspot.com.es/search?q=darwinism

    It is a blog of the coincidences I have experienced which I found the most striking.
    Seeing that I run such a blog, you will hardly be surprised to learn that, whilst subscribing to no faith, I am a Deist, dualist and am also sympathetic to ideas of vitalism.

    You say that you´re unhappy with accusations of lying.
    Well, when I challenged Dawkins at the http://www.guardian.co.uk site that he had campaigned to suppress a commissioned anti-Darwinian article by Richard Milton (an exchange which is still there) he denied it.

    The incident is outlined here –
    http://www.lauralee.com/milton2.htm

    I have taunted Dawkins with it loads of times on Twitter. Often others have then gleefully retweeted it.

    Milton says staff at the paper testify that Dawkins told the editor that if she went ahead and published his piece he would “…bring every scientist in the country” down against her.

    Somebody´s lying there, Dave. I wonder who?

    World´s number one thinker? My arse.

    Moving on then to your specific challenges re cytochrome c(other claimed genetic evidence for neo-Darwinian evolution such as chromosome 2, viral insertions, etc has hardly been touched upon by myself in Twitter debates)- here´s a better retort than that of the Creationist vid I swiftly cited when challenged by someone else to say something on this subject.

    It is from Milton´s book –

    “Research showed that the sequences of amino acids comprising these proteins varied slightly from species to specis. This seemed enormously promising for it appeared to show a variation at the molecular level between species that would mirror the morphological differences in the anatomy of those species. Although fossils and comparative anatomy had failed, biochemistry could perhaps provide the evidence Darwinists sought of patterns of evolutionary inheritance.
    … … …
    Perhaps by compiling a table of sequences of all the common proteins for all species we could get a quantified numerical picture of how closely or distantly related each species is?
    This hope, too, was dashed. According to Michael Denton,

    As more protein sequences began to accumulate during the 1960s, it became apparent that the molecules were not going to provide any evidence of sequential arrangements in nature, but were rather going to reaffirm the traditional view that the system of nature conforms fundamentally to a highly ordered hierarchic scheme from which all direct evidence for evolution is emphatically absent.

    What biochemists found when they compiled their table of proteins (such as cytochrome c) is that it is possible to classify species into groups and that these groups do indeed correspond exactly to the groups that have been arrived at by comparative anatomy. However, what is most striking about such a protein ´atlas´ is that each of these identifiable groups or subclasses is isolated and distinct from the others. There are no transitional or intermediate classes, just as there are no transitional species in the fossil record or in the living world today.
    Denton points out that published tables of divergence of the cytochomes, such as the Dayhoff Atlas of Protein Structure and Function, illustrate this dramatic absence of intermediates.
    The most primitive organisms are bacteria whose cells do not not contain a nucleus. All higher organisms, from yeasts to humans, whose cells do contain a nucleus, are called eukaryotes. If all eukaryotes have descended from bacteria, then you would expect to find a gradual divergence in their proteins like cytochrome c. In fact what you find is that all the main classes, from man to kangaroo, from fruit fly to chicken, from sunflower to rattlesnake. and from penguin to baker´s yeast, are all equidistant from bacteria with around 65 to 69 per cent divergence.
    According to Denton,
    Eucaryotic cytochomes, from organisms, as diverse as man, lamprey, fruit fly, wheat and yeast, all exhibit a sequence divergence of between sixty-four per cent and sixty-seven per cent from this particular bacterial cytochrome. Considering the enormous variation of eucaryotic species from unicellular organisms like yeasts to multicellular organisms such as mammals, and considering that eucaryotic cytochromes vary among themselves by up to about forty-five per cent, this must be considered one of the most astonishing findings of modern science.

    Even more extraordinary is the complete absence of evidence from biochemistry for the most basic Darwinian evolutionary scheme of fish to amphibian to reptile to mammal. When the protein divergence of land-dwelling vertebrates – amphibians, reptiles, mammals – are compared with those of fish, they are all again equally isolated. There is no graduation of divergence as one would expect in an evolutionary sequence.
    The horse, the rabbit, the frog, and the turtle are all 13 per cent divergent in their cytochrome c from the carp. “At a molecular level”, says Denton, “there is no trace of the evolutionary transition from fish to amphibian to reptile to mammal. So amphibia, always traditionally considered intermediate between fish and the other terrestrial vertebrates, are in molecular terms as far from fish as any group of mammals.”

    Battling it out with genomic evidence only happened comparatively recently in the debate.

    ” This shift in emphasis has occurred not only because of the attraction of the new biology as holding the answers to many puzzling questions, but also because the traditional sciences had proved ultimately sterile as a source of decisive evidence. The gaps in the fossil record, the incompleteness of the geological strata, and the ambiguity of the evidence from comparative anatomy ultimately caused Darwinists to give up and look somewhere else for decisive evidence.”

    One of the oddest things is that animals which look and behave very similarly may have enormously different DNA coding. e.g. there are about 800 different types of frog, but the DNA amongst them differs more than that between a bat and a blue whale.

    James

  2. Thanks for taking the time to comment, James.

    > First of all, and to correct what you have blogged, I do not think the
    > cytochrome c comparison evidence to be anything like one of the
    > strongest points against neo-Darwinism and have recently said as much on
    > Twitter. I addressed it there because someone had challenged me about
    > it.

    Ah OK, I thought you wanted to talk about it (from the Tweets I quoted).
    I was therefore expecting a knockout blow in the video, or at least a
    reasonable swing at it, and was a bit surprised at what you wanted us to
    look at.

    > The immediate problems that I always had with the idea, from a very
    > young age, were

    I’m not sure I understand the nature of those problems, but if we could
    stick to the cyt c issue for the moment that might help. You’ve raised a
    fearsome number of issues, and I’m keen to nail just that one first.

    > But how does Darwinian thinking sit with creatures which have complex
    > life cycles and/or undergo metamorphosis? e.g a caterpillar?
    >
    > As far as I´m concerned a butterfly refutes modern evolutionary theory.
    > No further evidence required.

    OK, that I did understand, but I don’t think there is a problem.
    Specialisation and evolution can go on in different directions in
    different stages of the life cycle of an insect (or other organism).
    Adult organs and behaviours often get put on hold until you’re big
    enough to take them on. It’s not different, in principle, from the fact
    of puberty, the later development of secondary sexual characteristics in
    humans. The early stages (nymphs) of locusts are quite different from
    the adults, being sexually immature and flightless; butterflies have
    taken that specialisation to a much greater degree.

    > Or the doppelgangers of Australia where, with the exception of the
    > reproductive systems, we have exactly the same animals in terms of
    > wolves, rats, etc which have come about, the leading Darwinists of the
    > 20th century assured us, through nothing more than adaptation and
    > natural selection. They also, quite by themselves, refute modern
    > evolutionary theory. No further evidence required.

    Most biologists would regard the appearance of these similar bodily
    arrangements (as similar solutions to similar problems) as good evidence
    *for* evolution. If you’re going to crawl through tunnels in the earth
    after your food, you are better off becoming long, thin, and flexible,
    whether you be an earthworm, a snake, a caecilian (a legless amphibian),
    or whatever. Same goes for other ecological niches, such as those
    occupied by placental or marsupial wolves, rats or moles.

    > Those two still remain perhaps the biggest problems for me when asked to
    > accept a theory of gradual change.

    I hope you can understand why I don’t see either of them as problems,
    even if you don’t accept the arguments. But I don’t really want to take
    either of those issues on any further until I’ve got the hang of where
    we come apart over cyt c.

    > You say that you´re unhappy with accusations of lying.

    I’m very unhappy with Wile’s general accusation that evolutionary
    biologists routinely lie about cytochrome c. I really don’t think they
    do. I think that’s a terrible thing to say about them and I don’t think
    there’s any reason for it. And unless you also think that evolutionary
    biologists are lying about cyt c, I’d suggest you stop pointing people
    to that video clip. (And thanks to your comments, I now think Wile is
    just re-describing Denton’s argument, so I’ve lost any other interest in
    talking about Wile’s video clip.)

    You say, I think quoting Milton, who is in turn quoting Denton from 1985:

    > What biochemists found when they compiled their table of proteins (such
    > as cytochrome c) is that it is possible to classify species into groups
    > and that these groups do indeed correspond exactly to the groups that
    > have been arrived at by comparative anatomy. However, what is most
    > striking about such a protein ´atlas´ is that each of these identifiable
    > groups or subclasses is isolated and distinct from the others.

    Distinct but not isolated. Human cyt c and rhesus monkey cyt c differ by
    a single amino acid; human cyt c and chimp cyt c by no amino acids at
    all. The primates differ from all other mammals at a number of
    positions, and in the same ways. So we think that fits with a view that
    primates have a common ancestry, and that humans and chimps share a more
    recent common ancestor with each other than they do with monkeys. Not
    only does it fit with a view of evolution, but alternative explanations
    are hard to find.

    > eukaryotes. If all eukaryotes have descended from bacteria, then you
    > would expect to find a gradual divergence in their proteins like
    > cytochrome c.

    I tried to explain this misconception in my earlier piece. Let me have
    another go.

    The idea is, the sequences of molecules of related organisms can ‘drift’
    from an ancestral sequence, and the longer ago they separated, the more
    differences will accumulate. Now, differences will accumulate in both
    the bacterial line and in the eukaryote lines, so modern bacteria and
    modern eukaryotes will each differ from the ancestral bacterium, perhaps
    by a similar amount. Similarly, mammals and frogs will each end up
    accumulating a number of differences from the sequence of an ancestral
    fish, and *so will fish*. The picture is of a branching tree, of which
    we see the uppermost twigs; it’s not a ladder where we have all steps
    preserved, and where fish sequences are preserved looking as they always
    did.

    > “At a molecular
    > level”, says Denton, “there is no trace of the evolutionary transition
    > from fish to amphibian to reptile to mammal. So amphibia, always
    > traditionally considered intermediate between fish and the other
    > terrestrial vertebrates, are in molecular terms as far from fish as any
    > group of mammals.”

    That’s exactly the misconception. If Denton thought that was a problem,
    he was looking at the evidence in the wrong way. (In all fairness, I
    think the penny has dropped with Denton, but people are still using his
    old arguments.) The cyt c of amphibians has been evolving away from that
    of ancient fish as long as those of mammals. But the cyt c of modern
    fish has been drifting away from that of ancient fish as long as either.
    What you should get – and what you do get – is not intermediate
    sequences, which aren’t around any more, but shared differences within
    modern groups. The sequences say, “I’m a tree” but not “I’m a ladder”.

    The penny dropped? I believe Denton these days does not dispute the idea
    that molecular evidence is consistent with a branching tree, and agrees
    that it suggests that evolution has happened. [“In the case of primate
    DNA, for example, all the sequences in the hemoglobin gene cluster in
    man, chimp, gorilla, gibbon, etc., can be interconverted via single base
    change steps to form a perfect evolutionary tree relating the higher
    primates together in a system that looks as natural as could be
    imagined. There is not the slightest indication of any discontinuity.”
    (Denton, Nature’s Destiny, 1998, p.277) ]

    > “as a source of decisive evidence. The gaps in the fossil record, the
    > incompleteness of the geological strata, and the ambiguity of the
    > evidence from comparative anatomy ultimately caused Darwinists to give
    > up and look somewhere else for decisive evidence.”

    Well, hardly, but that’s a discussion for another day.

    > One of the oddest things is that animals which look and behave very
    > similarly may have enormously different DNA coding. e.g. there are about
    > 800 different types of frog, but the DNA amongst them differs more than
    > that between a bat and a blue whale.

    That sounds like a bit of a gloss, why the ‘but’? I don’t know the
    evidence that this claim is based on (citations always welcome), but
    even if it’s true, frogs have been around and evolving in their various
    ways around the world for 250 million years, while the most recent
    common ancestor of bats and whales lived around 100 million years ago,
    and an awful lot of the bits of a bat you can find in a whale. So if we
    think only about drift in molecular sequences (and not about natural
    selection), that is exactly what you would expect. But still, let’s not
    do much more work on that issue until we have got the story straight
    about cyt c.

    • P.S. I think there has been some random drift in the claim about frogs; there are estimated to be thousands of species of frogs & toads (there’s no real difference), maybe 5,000, not 800.

      • er,,, yes: number of frogs was quite wrong.
        I stand by everything else though and all points you have made against here, in your various posts, to be addressed soon.
        J.

      • Fine, no rush, but if you try and respond to every single point, you might do yourself an injury; I invite you start with the interpretation of the molecular evidence/cytochrome c. I just can’t imagine how the best interpretation of those data is not ‘an evolutionary tree’.

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