Commentary on the so-called Creation/Evolution/Intelligent Design Debate and Right-Wing nuttery in general - and please ignore the typos (I make lots!)

Tuesday, January 31, 2006

More software engineer genetics from R. David Pogge

I never know whether to laugh or cry when I read things like this.
R. David Pogge, whose site contains silly articles on evolution (a few of which I have rebutted already), seems to believe that one can successfully take the concepts of information theory and apply them directly to genetics in the same way that the concepts are used in electronic communication and software.
And comedy ensues...
My comments in red.
===========================================================


Gene Duplicatioioion
Added genes don’t add information.
Interesting. So now even adding new genes doesn't add information to the genome? Another example of creationists trying to "disprove" evolution via definition...


Last month, we shared Jeff’s email about gene
duplication
with you. Argumentative Alex responded immediately with an email
titled, “Gene Duplicatioioion”. We presume the doubly repeated “io” in the title
was intentional. It was funny, but it helps make our point, not Jeff’s. The
repeated letters do not increase information.


Not in written English words, no.

In our column we had written, “We hope he got the point.” Alex picked up
this phrase and responded:

We hope he got the point.
We hope he got the paint.
We hope she got the paint.
We hoped she got the paint.
He hoped she got the paint.
He hoped she got the paints.
She hoped she got the paints.
She hopped, she got the pants.
She shopped, she got the pants.
She shopped, she’d got the pants.
She shopped, she’d get the pants.
How long would [you] like
me to go on?
Best wishes

Alex

We didn’t believe that all of those changes were random. We thought
that Alex cleverly (dare we say, “intelligently”?) made each change with the
expressed goal of changing the meaning to prove a point. When we challenged the
randomness of the process, Alex replied,

No, I confess, the changes were not random - I don't
have geological time and had to use a bit of intelligent design. However, if you
don't mind waiting for a bit I could do the same thing by changing or
deleting one letter at random. If I deleted the 'failures' and sent you
only the sentences that pass my 'natural selection' test, you would not be able
to tell the difference!



Alex has confused an inefficient process with a random process. If I
didn’t mind waiting a bit, I could have a monkey randomly press keys on my
keyboard. Every time the monkey presses the wrong key, I could delete it.
Eventually “the monkey” could write this whole column “randomly.” But, in fact,
I would have been guiding the process all the way, making the monkey write what
I wanted it to write. It would just take a lot longer than pressing the keys
myself.



Now, replace the monkey with, say, an imperfect DNA replication system, and you deleting entries you did not want with nature applying selection pressure to "delete" the deleterious results of the imperfect DNA replication, and thus we have an imperfect yet far more analogous situation. But please, go on...


Each of Alex’s intentional modifications was syntactically correct. That is, all
of the words were spelled correctly. Each intentional modification was
semantically correct. That is, the nouns and verbs were in the correct
positions. But information did not increase.


It will be interesting to see how Pogge deals with "information." In my experience, if you ask 10 creationists - even 10 with engineering backgrounds - what "information" is you will get 10 different answers. But I do wonder if Alex's point was even to show an increase in information. It is hard to tell.


We hoped he got the point. We didn’t hope he got the PAINT. Alex’s first
modification did not accurately express anything about our hopes. Therefore, it
did not convey information. We didn’t hope SHE got the paint, either.


So, it appears that to R. David Pogge, creationist software engineer, that "information" means 'meaning.' Strange definition for an engineer to use, considering what "information " really means in his own field:

"Information is a message from a sender to one or more receivers. If information is viewed in this manner, it does not have to be accurate. It may be a truth or a lie, or just the sound of a kiss. Even a disruptive noise used to inhibit the flow of communication and create misunderstanding would in this view be a form of information..."

More interesting is the measure of information as used in Information Theory, which Pogge mentions knowing all about in other essays:

"The sequence below would have a very low algorithmic information measurement since it is a very predictable pattern, and as the pattern continues the measurement would not change. Shannon information would give the same information measurement for each symbol, since they are statistically random, and each new symbol would increase the measurement.
123456789101112131415161718192021 "


So, according to Information Theory, even 'random' symbols increase information.

Yet Pogge declared that altering the sentence presented by Alex, even randomly, even with the addition of symbols (letters, in this case), would not increase the information.
Hmmm.... Who to trust?


Truth matters, at least in the context of information transfer. There are two
things present in any transmission channel. One is “signal,” the other is
“noise.” Signal is defined (by engineers) to be the information one wants to
transmit. Noise is defined as anything that prevents that information from being
transmitted. What Alex actually did was to decrease the signal-to-noise ratio by
changing “point” to “paint.” Because of that increase in noise, information was
lost. The receiver no longer knows that “We hope he got the point.” The receiver
incorrectly thinks “We hope he got the paint.” Each of the changes Alex made to
our transmission simply increased the noise, so that the message was totally
garbled at the end.



Providing that the original message was the only one that the receiver would want/could understand. Alex's little example may not have any relevance to "increasing information", but it is more analogous to what happens in the genome than is this notion set forth by Pogge that changing the message decreases information and thus negatively impacts evolution somehow. It would benefit Pogge to try to learn some basic genetics and biology. The problem is, if he were to do this, he would lose his plausible deniability. That is, he could not feign ignorance when his disinformation is laid bare. Can't have that.


You may have played a party game, where a dozen or so people line up. The first
person whispers “We hope he got the point,” to the second person in line. The
second person whispers it to the third person, who whispers it to the fourth,
etc. Finally the last person says the message was, “She shopped, she’d get the
pants.” Inaccurate transmission from one person to another caused information to
be lost.


Hmmm... "We hope he got the point" is certainly different than "She shopped, she got the pants". But I am not sure that it contains less meaning. The only way that this would be true (that information was lost) would be, again, if the original message was the only one that the receiver wanted/could understand. This has little relevance to genetics.


Engineers never intentionally introduce noise into a communications channel in
the hopes that more information will appear.


Good for engineers. What does this have to do with genes and evolution?

There was information in “We hope he got the point.” There was meaning that we
wanted to convey. There is no truth to the statement, “She shopped, she’d get
the pants.” Since it isn’t true, there isn’t any information.


What? How does Pogge know that the message isn't true? And what does "truth" have to do with information? Nothing. Lies, disinformation, etc. are "information" in the colloquial sense, too. Just read Pogge's creationist website and see for yourself!


Information was lost in the modification of the message.
The claim is made by
evolutionists that random insertion, deletion, and modification, of the bases in
a DNA molecule changed reptile DNA into mammal DNA. That is, these random
changes caused breasts to form, and furthermore, random changes caused these
breasts to lactate at the end of pregnancy.



Like most creationists, Pogge leases out (at least) half of the equation - the random modifications that did not work out, that are harmful, etc., are lost. Purged from the population.
Oversimplifying concepts (changed reptile DNA into mammal DNA) and making unwarranted extrapolations of engineering concepts is a poor way of producing "scientific" rebuttals .


People like Alex think that, given enough time and enough
lizards, this could happen. They think we just didn’t see all the lizards with
non-functional breasts because natural selection eliminated them immediately. We
think this is an unscientific belief.


We - we being people with appropriate backgounds and knowledge - believe that people like Pogge rely too heavily on folksy pseudologic and disinformation to try to prop up their beliefs. We know that conjuring up lizards with non-functional breasts plays well in the pews and with the dimwits that think the same way Pogge does in the first place, but to those with some basic, relevant knowledge, it comes across as sophomoric nonsense. And that makes us question the integrity of those that engage in such antics.
Of course, people like Pogge believes that fully formed modern humans were created from dirt no more than 10,000 years ago. We KNOW that this is an unscientific - and irrational - belief.

Friday, January 27, 2006

An ineffectual rebuttal (Baraminology)

*The following is still in draft form and may contain typos and incomplete thoughts. I plan on 'finishing' it over the weekend and will add links and such where helpful*

Crevo linked to an old discussion board post I had written in which I had briefly critiqued a 'peer reviewed' creationist article on the subject of Baraminology. He rebutted it, and below, I respond to his rebuttal. My replies in red.


The primary article under discussion is "A Quantitative Approach to Baraminology With Examples from the Catarrhine Primates". I don't have access to the article, so I'm going to give the authors the benefit of the doubt. It's possible they don't deserve it, but I've read other things by Cavanaugh, and so giving him the benefit of the doubt seems reasonable to me.

The basic error in the criticism is a category error. Two of them actually. The first and most important one is that, while the author appears to understand the difference between assumptions and conclusions at the beginning of the article, he appears to forget it by the end.


Is this really what I did? Or did I expose the baraminologist/creationist penchant for conflating and confusing the two? We’ll see…



There are multiple kinds of creationist scholarship. Some of it is geared towards proving the creationist position. Other works are scholarship that research _from_ the creationist position. This paper, as far as I can tell, is the latter. It does not say "the results of this paper show that humans and chimps are different baramins", instead it says "we know from scripture that humans and chimps are in different baramins, and we can use that information to help us determine which characters and character analysis techniques are useful in determining baraminic organization". Those are two completely different statements. The paper appears to be making the latter, while the article appears to be criticizing it for making the former.


The baraminologists start with the assumption that Scripture is correct, then use this assumption as a framework for their analyses. However, they later use their analyses to lend support to their assumption. This is clearly demonstrated by me in the criticism.




The author of the article complains that the paper hand-selected the traits that put them in different baramins, but in fact that was the entire point of the paper -- to determine what traits were important baraminologically. If humans and chimps are in different baramins, then it is reasonable to examine the differences between them and use them as guides to determining baraminically important characters.

And so Crevo endorses cherry-picking data to get preconceived conclusions.
Apparently, Crevo accepts that things like where a creature lives is more important than their genetic make-up in determining their ancestral and descendant relationships.



Now, the question is, are creationists alone in arguing from assumptions to conclusions? The answer is no. For example, see the paper Estimate of the Mutation Rate per Nucleotide in Humans. This paper estimates the rate of nucleotide change. However, it does so by comparing chimps to humans. Thus, the counts in that paper are based on the assumption that chimps and humans share a common ancestor.

There is a major difference here, that Crevo is glossing over. The “assumption” of human-chimp ancestry is actually a conclusion based on multiple lines of empirical evidence, while the assumption that humans are special creations separate from all other animals is premised solely on Scripture. Further, the goal of the Nachman and Crowell paper is not to ‘prove’ or support human evolution, rather it is to examine mutation rates. The baraminology paper, on the other hand, presents it’s rigged findings to support their assumptions.



I have seen this paper used to argue that this overcomes Haldane's dillema by showing emperically that the mutation rate is fast enough.



Creationists, including Crevo, utterly misrepresent the impact of 'Haldane's Dilemma'. Their use of it is premised solely on their flawed assumptions. See this.



However, this is a totally inappropriate use of that paper, because the paper is only correct if chimps and humans share a common ancestor, which is the point under discussion. Thus, it is circular reasoning. Note that it isn't the paper that was guilty of circular reasoning -- in fact the paper is an excellent example of scholarship. It is using the paper in a way that confuses assumptions and conclusions that is inappropriate. There is nothing wrong with taking assumptions and using them to press forward. Ultimately we have to. The problem comes when we confuse our assumptions and conclusions, and when science sets a pre-determined set of assumptions for everyone else to follow.



Indeed…



I have no problems with evolutionists using evolutionary assumptions for research. It doesn't make the research bad or useless or inappropriate. However, it is bad if people take the assumptions and confuse them for conclusions.

And that is what this author does.

The authors of the baraminology paper, yes.


Let's look at the concluding statement:

"That is, they have to pick data that give them the results they want – those that conform to Scripture."

Note that this isn't about getting a _desired_ conclusion. The conclusion is what are the baraminically important characters -- that list of characters did not come from scripture. The _assumption_ is scripture. This is one of the hallmarks of baraminology -- that it doesn't attempt to argue for or against the scriptural perspective, but simply uses it as an assumption for ongoing research.

Incorrect. As Crevo has not read the paper – and I have – I know this is incorrect. The authors start with Scripture, they then essentially discard the analytical results that do not conform to their assumptions. They then conclude that their now cherry-picked results DO conform to Scripture, so everything is hunky-dory. Crevo should not be engaging in fellow creationist protection like this unless/until he actually reads the paper.



I can see why others may not like it, specifically those who don't see scripture as authoritative. But the specific criticism being thrown at this particular paper seems to be coming from the confusion between assumption and conclusion.

It has nothing to do with ‘not liking it.’ No, my criticism stems from the fact that they cherry-picked data to get the results they “knew” were correct. I explained how I concluded that fairly explicitly. Briefly, they excluded objective data – data that they had used with great praise in previous papers – because it did not provide support for their assumption, and embraced subjective and largely irrelevant data because – and only because – it gave them what they hoped for. In addition, as I explained in the article, the authors were aware of a paper that was far more rigorous and used far more morphological data then they did, yet did not cite it because, I believe, the results did not conform to their assumptions.
If researchers have to discard and ignore data analyses because they do not support/conform to their assumptions, does not the valid conclusion become that there is a problem with the assumptions?



If this paper had been an attempt to prove that primates were in a different baramin than humans, then the criticism given in the article would be completely valid. However, as it was using it as an assumption, it is not.

It is true that establishing the separate baramin for humans was not a stated goal of the paper, yet it was stated clearly in their conclusions (and in the abstract) that this was a result. An oddity – they start off stating the assumption of the supremacy of the “Scriptural criterion” which indicates non-descent for humans, then later use data analyses to try to ‘confirm’ it.





As a short, non-proving defense of the assumption, let me ask a question -- if God created individual kinds, don't you think His scripture would be the best initial source of information as to what those kinds are?

If the assumption was borne out by other lines of evidence, perhaps.


A separate, and much more minor error in the article deals with his criticism of what determines appropriate traits for analysis:

"Things like percent foliage in diet, monogamy, population group size and density, home range size, etc. It looks to me like these data too were chosen to produce a desired outcome, for what exactly does “monogamy” have to do with descent?"

This misses the fact that creationists are not bound by descent being the only determining factor of the makeup of a baramin. A fairly minor point with little consequence, but I thought I'd point it out anyway.

In reality, the baraminologists accept descent, they just place arbitrary (i.e., premised on Scripture) limits on it.
If the baraminologists are not bound by descent, why on earth are they even trying to determine baraminological relationships? If God can just poof into (and out of) existence anything He wishes, isn’t trying to define these groups and their ancestral-descendant relationships a futile effort?

Monday, January 23, 2006

When all you have is a hammer.... [Pogge again...]

... EVERYTHING is a nail.

R. David Pogge is an electrical engineer and a creationist. He maintains a website that purports to provide information that 'evolutionists don't want you to know '.
The webite is, however, more of a clearinghouse for propaganda and disinformation, and I have written a few articles about the sort of hogwash you can expect from Pogge.
However, creationists with engineering backgrounds - specifically, electrical or computer engineering backgrounds - seem to have a tendency to assert that "they understand thermody­namics, probability, system design, and information theory" and therefore have some sort of unique insight into... biology.

Well, let's see if Pogge's knowledge of thermodynamics, probability, system design, and information theory REALLY provides for him some special insight into things that have nothing to do with electrical engineering.

===========================

Gene Duplication
More of the same.

On several occasions we have said that new genetic information
cannot arise by chance. Jeff disagreed. He said,
Actually new information can appear in the genetic code by gene
duplication. An interesting article outlines a study of Colobine monkeys and a gene duplication. The study was done by Jianzhi Zhang of the university of Michigan.
http://www.sciencedaily.com/releases/2002/03/020304081153.htm.
We replied,
“genetic code by gene Actually new information can appear in the
genetic code by gene duplication. Jianzhi Zhang An interesting article
Actually new information an appear outlines a study of Colobine monkeys and a gene duplication. The study Actually new information can appear was done by Jianzhi Zhang of the university of Colobine monkeys Colobine monkeys Michigan.”

We hope he got the point. Random repetition of words does not increase information. If you buy two copies of USA Today, you won’t get any more information than if you just bought one. Furthermore, the redundant words tend to increase confusion, not knowledge.
Incredible. In one short, arrogant little essay, Pogge nicely demonstrates the danger of directly applying one field of knowledge to another. Don't get me wrong - I do not dimiss the potential benefits of thinking 'outside the box' and the like. What I find silly is the fairly common antic of creationists with engineering backgounds to declare without doubt that information theory, etc., as they use and understand it, applies directly to genetics and gene expression.
Sure, merely duplicating lines of text in an email or a news article will likely only confuse. I assume the same is true of lines of code in computer software in most applications. Similarly, putting more of a particular word into a sentence will likely not change the meaning of the sentence:
"The study was done done done by Jianzhi Zhang ..."
Unfortuantely for Pogge and a host of people that employ similar "reasoning", genes do NOT, in fact, work just like lines of text in written English or computer software.
It would also appear that Pogge did not bother to read the linked-to article, because after all, he is a creationist engineer, and he KNOWS that gene duplication is irrelevant... But if he HAD read the article, he would have seen things like:
"Of the more than 40,000 genes in the human genome, for example, about 15,000 appear to have been produced by gene duplication....
Most primates have one gene encoding the enzyme, but the researchers found that the douc langur, a colobine monkey from Asia, has two---one encodes RNASE1, and its duplicate encodes a new enzyme, which they dubbed RNASE1B.
... Zhang's analysis shows that the duplication occurred some six million years after colobines began eating leaves. "So leaf-eating did not depend on the new gene, but the new gene apparently improved the efficiency," he concludes. "
But we wouldn't want Pogge to spoil his certainty by considering scientific information...
Gene duplication can result in a number of things, and not merely 'confusion.' For example, duplicating a gene could double the amount of a particular protein product. Depending on when that happens, a number or very real phenotypic or metabolic changes could occur.
That is, the "meaning" of the information has changed despite it being merely being "redundant."
Similarly, increasing a gene's expression can produce not only metabolic effects, but beneficial metabolic effects.
So, in reality, genes and their expression and effects are, at best, only superficially analogous to written words or lines of computer code. Unfortunately, people like Pogge do not bother finding out such things, instead relying on their certainty that what they know trumps all, and the belief that mere superficial analogies are sufficient to 'disprove' established scientific facts.
Such is the way of the internet creationist.
*Pogge received another message on this subject and wrote a similarly simplistic bit of gibberish in reply. I will respond to that shortly.

Friday, January 20, 2006

R. David Pogge and his 'Mutation Math' email

R. David Pogge posted an email he received in response to his essay Chimps are like Us, which I have already rebutted. The email's author, "Doug", agrees with Pogge's claims but expands on them, much to Pogge's glee. Let us see if the glee was warranted...
==============================================================
Mutation Math

It is difficult to compute exactly how different two strands of DNA are.
We are going to comment on this email before you read it because, frankly, we are afraid you might not make it all the way through the email. Math turns some people off. This is why we try to avoid using mathematical arguments whenever possible. But, in the
October newsletter, where we talked about the published 4% difference between human DNA and chimp DNA, the devil made us do it.


Indeed. Apparently, the Devil made R. David Pogge produce intellectually dishonest propaganda in a sad attempt to prop up his religio-political ideology by attacking evolution.

Evolutionists were minimizing the difference between us and chimps to try to prove we have a close common ancestor. We wanted to show that the difference is really very large, and that one can present numbers in a variety of ways to minimize or maximize differences.
No, evolutionists were analyzing the difference, and Pogge engaged in some silly tomfoolery to try to minimize what data analyses indicate.
Doug argues that the differences are actually even larger than we said, and uses a mathematical argument to back up his position.
As is par for the course in creationist writings, his “mathematical argument” is, as was Pogge’s original diatribe, premised on a substandard understanding of the issues.

We suspect most of you won’t be able to follow it.

Because, after all, creationist software engineers know all about everything, and they know that you commoners are just too dumb to understand this stuff. That is why you will just have to believe whatever R. David Pogge tells you to think. Bad move.



We present it to you primarily to show just how difficult it is to make sense of the numbers.

=========================================================
Hello,
You might be interested in some explanations for some of the details related to the recent Newsletter. They actually strengthen your case.
The 35 million substitutions represents ~1.25% of the genome. The remaining 5 million indels are, on average, roughly fifteen bases long. This means that there are about 75 million bases (i.e., ~2.75% of the entire genome) accounted for by these indels. The sum of these is 4%. Some of these indels are hundreds of bases long. And many of them involve complex additions to the genome ( i.e., not simply the replication of an existing genomic neighborhood). Note that such indels should NOT be treated as if they are a single mutation event.


Here is where “Doug” demonstrates a typical creationist trait – making an incorrect claim yet stating it as a fact. The real fact is that indels ARE, and should be, treated as one time events.

For example:
abcdefghij <- originalabccccccdefghij <- single indel/single mutationabcdefghdefghij <- single indel/single mutationabcindeldefghij <- single indel/multiple mutations

Case in point – ‘Doug’ presents multiple scenarios – multiple events – as indicating a single one! In a single indel with multiple mutations, the indel itself is still just a single event. ‘Doug’, like Pogge and others, is trying to muddle things up with creationist math.

… some information addressing another point you made on "Chimps Like Us":
"DNA contains the biological instructions for making proteins. If 29% of the proteins are identical, that means that 71% are different, doesn't it? If the DNA is 96% the same, why are 71% of the proteins it produces different?"
Suppose we have two "alignable" genomes (i.e., no indels).

You can align genomes with indels just as you can align genomes without. ‘Doug’, like Pogge and most other creationists, clearly has no direct or relevant knowledge of the things he is discussing. As we will see below, he incorrectly believes that all mutations occur in genes. A fairly ignorant – yet common - belief among creationists.
the chance of a single bp being different is 4% (i.e., 1 - 0.96).Suppose that the chance of a single bp substitution effecting [sic] a change in protein is x.Suppose that the average number of bp's coding a single protein are N.Suppose that the chance of a protein being identical is 29%.

Whaa? Suppose? The 29% number is an empirical figure…

We have the following equation:(1 - 0.04x)^N = 0.29
I expect that you follow.

… that renders the above moot.

Finally, you mistakenly think that "[in] the last 4,000 years of recorded human history, there would have been about 20,000 mutations." In fact, the expected number of mutations would be proportional to the total number of humans born within the last 4,000 years!

First, Pogge’s original “estimate” of 20,000 mutations in the last 4,000 years was premised in his rather ridiculous interpretation of a sentence, which made him think that there must be a disproportionate number of mutations in the human genome (compared to the chimp).
Second, there is no relevance on the proportionality issue, since, for example, the rate of accumulation of neutral mutations is proportional to the mutation rate, regardless of population size. ‘Doug’ might have known this, had he any basic understanding of population genetics. But consider this - if a fellow creationist can find flaws in Pogge's reasoning, well...
Based on a stable pre-historic population size of one hundred thousand, we observe that the number of mutations experienced by that population in six million years is roughly the same as the number of mutations experienced by the historic human population in the last two thousand years (see http://www.census.gov/ipc/www/worldhis.html). In the first case, the population is compressed in size and expanded in time. In the second, it is compressed in time and expanded in size.

Which, again, is rendered moot by actual population genetics.
Note, however, that the same number of mutations does not indicate the same degree of evolution. Evolution requires the "fixation" of those mutations, and it likely requires the accumulation of numerous mutations (i.e., sequential mutation-on-top-of-mutation).

Erroneous assumption on top of erroneous assumption plus baseless assertion equals creationist certainty!
Not much else to say on this scienceagainstevolution.org travesty.

A Rose by any other name.... {Or, creationist Walter ReMine and his antics, part 1}

... Would still be a rose.




Walter J. ReMine is an electrical engineer and creationist.
This is one of what will likely be many installments on ReMine's claims, and will cover but one small aspect of the claims that ReMine likes to make.
He wrote a book, The Biotic Message, in which he argues, among other things, that a population genetics model proposed by J.B.S. Haldane in 1957 'disproves' evolution of humans from an apelike ancestor.
Strictly applying Haldane's model to human evolution over the course of 10 million years, ReMine claims that the "allowed" number of beneficial mutations that can become fixed (present at a frequency of 100%) , 1,667, is simply too few.

"Briefly. Haldane's Dilemma establishes a limit of 1,667 beneficial substitutions (where a substitution is almost always one nucleotide) over the past ten million years of the lineage leading to humans. The origin of all the uniquely human adaptations would have to be explained within that limit.
That is a serious problem. "


How does he know that 1667 beneficial are too few? Well, he just does.
Further, he accuses evolutionary biologists of trying to hide this "problem" from the public:

"Yet despite it being interesting, important, and easy to communicate, they did not inform the public. No, there was no conspiracy. But it was a staggering bit of negligence. Haldane's Dilemma is not just the problem itself, but also the evolutionists' negligence for not communicating it to the public. "


Of note here is this disclaimer: "No, there was no conspiracy."
This is of interest because he makes it quite clear in his book and in his many internet forays that he really thinks that there was a conspiracy. He doesn't call it a conspiracy, of course, and if you point out that what he is describing IS a conspiracy, he gets very indignant and as he has become known for, characterizes such clear inferences as "misrepresentation." But the way he describes it, it can really only be a conspiracy. Look at the above quoted section alone - he claims that 'Haldane's dilemma' is important, interesting, etc., yet THEY [evolutionists] DID NOT INFORM THE PUBLIC. Never mind the fact that there seems to be no reason TO inform the public about such things, and mind even less the fact that the issue was in fact discussed quite freely in the literature for some time and can be found in one form or another in many if not all population genetics textbooks. But THEY knew about it, and held it from the public. By definition, a conspiracy is evident when 2 or more people take part in an action that is illegal or harmful. THEY implies 2 or more people, and THEY did not inform, i.e., 'harmed', the public. Seems pretty clear to me.

Anyway, this particular post will deal with an offhand statement I wrote in this article, "Further, in his terrible book, he implies that it would take more than 500,000 such changes if evolution were true.* "
I asterisked this because ReMine claims that what I wrote is a misrepresentation of him (surprise, surprise). In a subsection of the above linked webpage titled 500,000 substitutions?, ReMine writes:

"My book had the ambitious goal of teaching this cutting-edge subject to the ordinary person. I therefore began my discussion with an uncomplicated scenario for tutorial purposes...
The figure "500,000" derives solely from the example itself (10 million years / 20 year effective generation time), and my goal of dovetailing this tutorial example easily into Haldane's example. Yet evolutionists misappropriate this figure. "



He finishes the '500,000 mutations' section with the following (which, if you have encountered ReMine before or read his book' contains some really funny stuff ):

"However, some of my evolutionary opponents seized that figure of "500,000 substitutions" as though it has some special role in my argument. It has none. It's purpose is solely tutorial, to teach, and to get the ordinary person thinking in population genetic terms — a subject most people hadn't thought about. The example simply reveals the mechanisms behind Haldane's Dilemma as understandable to the ordinary person. That also gets readers wondering why they hadn't seen such an obviously important topic before. ............

Throughout my book I avoid causing you to rely on my opinion, rather I cite leading evolutionists to support what I am saying. Or, I assemble the facts from evolutionists, and let you make up your own mind. This "de-emphasis of me," is key to making the book so compelling. This approach applies also to Haldane's Dilemma, where, for simplicity and authenticity, I advanced only one figure — Haldane's! It is essentially Haldane's figure.
The limit of 1,667 substitutions comes (in all its deepest respects) from Haldane. I merely framed it so the ordinary person can understand, and so evolutionists would have the most difficulty finagling around.
If you see anyone mis-representing the "500,000 substitutions" figure, then correct them on it, and send them here."



Now, let's think about that for a second. ReMine is claiming that his 500,000 mutatons figure is for 'tutorial purposes' only, and that evolutionists misrepresent him frequently. When I was first made aware of ReMine's site and read this section, I wondered why, in the first place, did he not present the actual section from his book which is the supposed source of evolutionist misrepresentation?
I will do for the reader what ReMine decided not to do - I will present his own words and let the reader decide if they think he was only presenting the 500,000 figure as a 'tutorial' for his readers:

"That's not a difficult calculation [deriving the 500,000 figure], yet it immediately reveals a problem. Is 500,000 beneficial nucleotides enough to explain the origin of humanity from some chimp-like ancestor? [..brief discussion on Haldane's model and ReMine's derivation of the 1667 number....] Is that enough to explain the origin of upright posture, speech, language, and appreciation of music, to name just a few of our uniquely human capacities? Is 1,667 beneficial nucleotides enough to make a sapien out of a simian?"

Now. let us juxtapose and interleave ReMine's 'disclaimer' about his 500,000 mutations figure with his 'explanation' for his claim of 'misrepresentation':

However, some of my evolutionary opponents seized that figure of "500,000 substitutions" as though it has some special role in my argument. It has none.
Is 500,000 beneficial nucleotides enough to explain the origin of humanity from some chimp-like ancestor?"
It's purpose is solely tutorial, to teach, and to get the ordinary person thinking in population genetic terms — a subject most people hadn't thought about. The example simply reveals the mechanisms behind Haldane's Dilemma as understandable to the ordinary person. That also gets readers wondering why they hadn't seen such an obviously important topic before. ............
Is that enough to explain the origin of upright posture, speech, language, and appreciation of music, to name just a few of our uniquely human capacities? Is 1,667 beneficial nucleotides enough to make a sapien out of a simian?"

If, as ReMine claims, his 'tutorial' was solely for instructional purposes for his readers, why on earth then would he write that THAT number is a "problem"? Why would he rhetorically ask if that number is enough when he claims his whole discussion is really about what he calls the Haldane number (1,667)?
It seems to me that ReMine takes his "fans" for granted. He apparently thinks that his readers cannot think for themselves - perhaps he even hopes that this is the case. For how else can one explain the facts:
1. ReMine does not quote his own work that is the apparent source of confusion, resulting in his critic's supposed misrepresentation of him
2. he claims that he only presented the 500,000 mutations figure as part of a "tutorial" for his, what he apparently assumes to be ignorant, readers
3. he claims that evolutionists are misrepresenting him when they claim that the 500,000 figure has a "special role" in his argument
4. reading what he actually wrote in his book, it is clear that he used the 500,000 mutations figure as a "set up" for his Haldane number


What do I mean by 'set up'? Consider the passage again:

"That's not a difficult calculation [deriving the 500,000 figure], yet it immediately reveals a problem. Is 500,000 beneficial nucleotides enough to explain the origin of humanity from some chimp-like ancestor?...
"Is that enough to explain the origin of upright posture, speech, language, and appreciation of music, to name just a few of our uniquely human capacities? Is 1,667 beneficial nucleotides enough to make a sapien out of a simian?"

First, he implies (via rhetorical question) that even 500,00 fixed, beneficial mutations cannot account for human evolution, then he delivers the death blow - he indicates that the "actual" number, 1,667, cannot, therefore, account for it at all.

I do not believe that any rational person can believe ReMine's "explanation." I think it obvious from the context of his actual writing that he implied that 500,00 fixed beneficial mutations cannot account for human evolution, and because according to his application of Haldane's model the number is substantially less, evolution is in big trouble.

========

to see Mr.ReMine in action, try this, if you have a high tolerance for arrogance and sycophantery...

Tuesday, January 17, 2006

Haldane's Dilemma - another creationist takes a blind stab

*This is in draft form and will be modified as needed*

**see also This new post in response to some nonsense at Dembski's blog

**UPDATE**
See bottom of article

Over at the Creation and Evolution blog, I have made a few comments to the blog's author, a computer programmer and creationist calling himself "crevo", after comments he had made regarding his article titled Evolution, Chance, and Design.

His comment that caught my attention was this:

"...Plus, you have the cost of selection, which limits the number of mutational events (of any type, not just base pair) between man and ape's most recent ancestor as being about 1,667, which is far too few. See Haldane's Dilemma."

The link takes you to a webpage authored by Walter ReMine, an electrical engineer and creationist, whereon he hawks his book "The Biotic Message". I will be writing up an article on my encounters with ReMine and his claims later, so I will not go into his book or his specific claims now.

But, I have encountered a number of people on the internet that employ ReMine's claims without question and what I have found is that they understand as little as ReMine does about this issue (for some concise information on Haldane's dilemma, see this article).

Crevo is one of these people.

I asked the following question of Crevo in response to the above:

"Please explain why, if that number is correct, it is 'far too few'."


And classic creationist comedy ensued. Crevo's responses in red, my replies in blue.

Round 1:
The number of mutational events that appear to have occurred between chimps and humans is in the millions. If you half that (since we are going from a common ancestor), you are still _far_ above 1,667.

You are completely unaware of what "Haldane's dilemma" actually indicates, that much is obvious.If you are going to refer to an issue like that, it seems reasonable that you should at least have an understanding of the basics.Haldane's model dealt with fixed beneficial substitutions, not all substitutions. As an example of how out of the ballpark your take on Haldane's dilemma is, consider this:
Any two humans differ by millions of substitutions. According to your take, no two humans can be related...

Round 2:
"Haldane's model dealt with fixed beneficial substitutions, not all substitutions."

That is correct, but do you honestly think that out of the millions of differences between chimps and humans, less than 1% of them are neutral? I'm also pretty sure that the differences I am quoting from are fixed in the population, but I will have to double-check.For more information, see:
http://www.nwcreation.net/wiki/index.php?title=CB121
=============

That is correct, but do you honestly think that out of the millions of differences between chimps and humans, less than 1% of them are neutral?

Um, no - I think that most of them are neutral. Please slow down and re-think your statement.

I'm also pretty sure that the differences I am quoting from are fixed in the population, but I will have to double-check.

No, they are not. In fact, they cannot be, for as I mentioned, any two humans differ by some several million nucleotides, therefore, it is impossible to determine how many substitutions, especially neutral ones, are in fact fixed.

For more information, see: http://www.nwcreation.net/wiki/index.php?title=CB121

You may have noticed that it is on a creationist site. ReMine the electrical engineer who has been misrepresenting the issue for years. For example, he claims that 1667 fixed beneficial mutations are too few. But he does not know what traits the ancestor had!
Therefore, simple logic dictates that he cannot know how many are too few. I know this because I have asked him on many occasions and he simply ignores the question. Further, in his terrible book, he implies that it would take more than 500,000 such changes if evolution were true.* This is, of course, quite stupid - the human genome only has 25-30-,000 genes! Further still, ReMine acknowledges that neutral mutations can also contribute to phenotypic differences and that they accumulate at a higher rate than do beneficial mutations, not to mention single nucleotide polymorphisms.

Round 3: I have replied twice, but so far, my replies have not been published on Crevo's blog (as of January 20). It may be innocent - he may just have not gotten around to accepting the comments, or, he may be refusing to publish them. So, I will comment here, in black.

"Um, no - I think that most of them are neutral. Please slow down and re-think your statement."

There was a missing "not" in that statement. Thanks for pointing it out!

"In fact, they cannot be, for as I mentioned, any two humans differ by some several million nucleotides, therefore, it is impossible to determine how many substituions, especially neutral ones, are in fact fixed."

No it is not. It would be based on sequencing a wide range of humans.

Let us recall what this is in reference to - Crevo had written that he was "pretty sure" that the numbers he was referring to are fixed in the population. However, the numbers he was referring to are in fact raw estimates premised on the comparisons of only a few individuals, and notice that he has now modified his original claim - he now says the number "would be" based on sequencing a wide range of humans. Meaning, of course, that he has unwittingly acknowledged that his claim is baseless. In order to determine which neutral substitutions are fixed in genes, we would have to sequence a very large number of humans, and this does not even take into account substitutions in intergenic regions nor those that are not expressed yet are part of the total number.


If the change exists in a wide sample of humans, it would be shown to be fixed.

By definition, fixation means that it is present in 100% of the population. But this is getting off topic.

Most of the differences between chimps and humans are fixed. There are 35 million base substitution differences, as well as 5 million insertion/deletion events (totaling about 40 million nucleotides).

In reality, it is quite likely that a large - a very large - number of those differences are in fact not fixed, for at least one of the reasons I mentioned before (polymorphisms between living humans). Even if all of those changes were fixed, the overwhelming majority are in noncoding regions and many that are in genes are neutral or nearly so, and so do not fall into the "dilemma" set forth by Haldane's model. Thus, flaunting these large numbers is at best a red herring.

"You may have noticed that it is on a creationist site."

Yes. In fact, I wrote it. So what? Are creationists wrong by definition?

No, they are quite often wrong on the facts, AND they tend to view the writings of other creationists unskeptically. The piece referred to is a fairly typical creationist "hero worship" job - Crevo simply repeats ReMine's claims and denigrates a few critics of ReMine's claims.


"ReMine the electrical engineer who has been misrepresenting the issue for years."

Really? I guess that's why the editors of peer-reviewed journals have been telling him they won't publish because the issue is already well-known?

Actually, the paper that you refer to is of substandard quality AND it says nothing new. I have read it. It was standard ReMine. Lots of finger pointing and sophomoric prose, very little of substance. Of course, ReMine's paper did not address his baseless claims re: Haldane's dilemma, so what we have is yet another red herring from Crevo.


"For example, he claims that 1667 fixed beneficial mutations are too few. But he does not know what traits the ancestor had!"

This is silly, because we know the number of mutational events between chimps and humans.

Ummm.... Ok. What does that have to do with the presumed ancestor? Surely, Crevo is not so underinformed (disinformed?) regarding evolution that he actually thinks evolution states that humans evolved FROM chimpanzees? In addition, only a tiny fraction of the mutational difference between humans and chimps represents phenotypic differences. Using Crevo's "logic" this would mean that because any two humans differ by some millions of mutations, that any two humans differ by some millions of traits. This is laughably absurd, yet Crevo is using as the crux of this portion of his argument!


Likewise, I would imagine that there would need to be at least that many changes just for going to obligate bipedalism.

Please name these changes. Please identify the traits that the ancestor did NOT have that the 1667 mutations must account for. But first, you will, of course, have to identify the ancestor. If you do not, how can you possibly know which traits had to be modified? Also, please explain how many beneficial mutations are required to produce a particular change.
If you cannot do at least the things I have mentioned, then claiming ANYTHING about Haldane's dilemma and numbers of required mutations is just empty rhetoric and sophistic gibberish.


"Further, in his terrible book, he implies that it would take more than 500,000 such changes if evolution were true. This is, of course, quite stupid - the human genome only has 25-30-,000 genes!"

Do you think genomes change an entire gene at a time? You should read Behe's peer-reviewed article about how long it takes just to change three _amino acids_.

No. You should read the Dover trial transcripts and see how Behe's peer-reviewed paper was shown to be little more than an academic exercise with little relevance to biology, not to mention evolution.
Of course, what we are seeing is the non-biologist's take on gene action. Non-biologists seem to believe - even insist - that any physical change requires some huge suite of 'beneficial' mutations. This is sheer ignorance.
One of my favorite refutations of this notion is the single point mutation in the FGF3-R gene that causes a form of achondroplasia (dwarfism). One little base pair substitution reduces the number of interphalangeal joints, produces disproportionate alterations in limb length, etc. Now, I am not presenting this as an example of evolution, nor as an example of a beneficial mutation. I am presenting this as evidence - proof even - that phenotypic changes do NOT in fact require large numbers of mutations. Those that claim that some huge number of mutations IS required are just telling stories to prop up their baseless claims.


In addition, the regulatory elements are not included in gene counts, and are just as important if not more so.

So perhaps that is why so many 'new' genes and the like are not really required, as creationists seem to insist?


In addition, a better count would be of proteins, not genes, which then goes into the hundreds of thousands.

If that is so, why do you even mention Haldane's dilemma? Of course, those proteins have to come from somewhere, do they not?

"ReMine acknowledges that neutral mutations can also contribute to phenotypic differences and that they accumulate at a higher rate than do beneficial mutations, not to mention single nucleotide polymorphisms."

This is true, but the rate of change would simply have to be astronomical, unlike any changes we've ever seen.

Really? Astronomical? You mentioned 40 million changes in the DNA. Humans and chimps are inferred to have separated from each other about 6 million years ago. That works out to about 7 changes per year, or about 140 per generation (based on a 20 year generation time, which is what ReMine used).
7 a year is astronomical? ~140 per generation is astronomical?
In reality, that is very close to the number gleaned from empirical studies.


The fact is, you are basically limited to 1,667 beneficial mutations. That's barely even enough to build a full gene, much less account for the beneficial differences between chimp and man.

The real fact is, you have no idea how many fixed, beneficial mutations would have been required to evolve humans from an apelike ancestor and continuing to claim that 1667 is too few is at best disinformative propaganda and wishful thinking.
***********************************

This morning (Jan.20) Fedmahn Kassad posted the following in Crevo's blog:

"I guess that's why the editors of peer-reviewed journals have been telling him they won't publish because the issue is already well-known?"

This is quite incorrect. Editors told him they wouldn't publish on another issue because it was on material that had been published 25 years ago. It wasn't about Haldane's Dilemma.

"The fact is, you are basically limited to 1,667 beneficial mutations. That's barely even enough to build a full gene, much less account for the beneficial differences between chimp and man."

Also quite incorrect. Since these are beneficial mutations, they are all gene modifying mutations. Walter has also acknowledged that in the same time, you could get 25,000 neutral expressed mutations. So, how many base pairs does this come out to be? I have gone a few rounds with Walter on this, using his own assumptions. Here is what Walter wrote: "Evolutionists do not get to assign the 1,667 mutations any way they please, say, as "regulatory genes" or as "mutations with a large effect". Nature does not work that way. Rather, the preponderance of mutations will be of the ordinary kind, with a small effect. Let me illustrate the concept with crude figures: about 1500 mutations with an ordinary small effect, 100 more for re-positioning genes on chromosomes (inversions and so forth), 60 as gene duplications, and 7 mutations to regulatory genes that have a larger effect "for a total of 1,667." The Human Genome Project estimates that the average gene consists of 3000 base pairs. Just taking Mr. ReMine's assumed 60 gene duplications, this would provide for 180,000 new base pairs not present in the common ancestor, and this is just from a small fraction of the 1,667 beneficial mutations. It is obvious that 1,667 beneficial mutations and 25,000 neutral mutations could add up to a great deal of base pair differences.The funny thing was that when I pointed this out to ReMine, he complained that I had misrepresented him. In dealing with him over the years, I have learned that anything he did not explicitly say - even if it is a given from his argument - amounts to misrepresentation if he doesn't like the outcome.
The Haldane argument is bunk, plain and simple. I have personally challenged ReMine to defend, and all he does is dodge and weave.

See: http://www.baptistboard.com/cgi-bin/ultimatebb.cgi/topic/36/111/4.html?

It will be interesting to see how - or if - Crevo responds.

Friday, January 13, 2006

"Hemi", for the last time.

Some folks just don't know when to stop.

Hemi is at it again. Knowing Hemi's antics as I do, this could go on for some time, each response of his focusing on some irrelevant minutae, on bits of information that have been explained to him a dozen times, on things that he just doesn't get. So, this will be my last reply to him, regardless of how much more absurdity he can regurgitate.
Hemi's rant in blue.


Pogge calculated a number of predicted mutations in the last 4,000 years. You ignorantly claim that prediction is a strawman. No it's not.

Yes it is, and I explained why. At least twice. It is premised on a, frankly, ridiculous interpretation of an offhand comment in a news article. Pogge "interpreted" this sentence:

"In some behavioral and cognitive traits, humans have changed dramatically since their evolutionary divergence from a common ancestor shared with chimpanzees."

to mean:

"The first sentence seems to imply something more like a 30/10 split rather than a 20/20 split because “humans have changed dramatically” compared to chimpanzees."

From this silly "interpretation", Pogge 'predicts' his farcical number. If you cannot see the silliness in that, then there is really little more I can do to help you. You are clearly in 'help my fellow creationist' mode now, and such a mode is impervious to reason.



All you did in your rebuttel to Pogge was accuse him of being dishonest and posted asinine sound bites to refute him.

'Sound bites'? You mean like where I posted entire paragraphs to illuminate Pogge's out of context quoting? My accusations of dishonesty (or incompetence) were supported with documentation, explanation, and links to source material when appropriate/possible. There is no need for a lengthy scientific rebuttal when an exposure of dishonest quote mining or bizarre and unwarranted interpretations/extrapolations can be demonstrated.


Since the 4,000 number is bogus, I asked you what was Your number. Surely your [sic] smart and have a prediction on how many mutations have occured in the last 4,000 years in the human species, after all you claim "we see them". And then, like the loud mouth no[sic] nothing you really are, you are claiming changes in genetic makeup you can actually see is not part of the phenotype.

That is correct. What is incorrect is your characterization of the issue. Yes, one can 'see' mutations by examining DNA sequence data, as I have linked to repeatedly. This, however, as has also been repeatedly explained to you, is not the phenotype. Phenotype is (emphases mine):

-The total characteristics displayed by an organism under a particular set of environmental factors, regardless of the actual genotype of the organism. Results from interaction between the genotype and the environment.

-What an organism looks like as a consequence of its genotype; two organisms with the same phenotype can have different genotypes.

-The visible characteristics of an organism resulting from the relevant coding of the genotype of the organism.

Ergo, 'seeing' mutations does not make them part of the phenotype, since they are part of the genotype.


You're just another loud mouth evolutionists [sic] that knows about half of what you pretend to know. Pogge, whoever he is, ran circles around you.

Hemi lacks a sufficient understanding of the material to warrant his coming to such a conclusion. Knowing little makes one very confident. Of note, Hemi is an auto body mechanic of some sort, not a biologist of any sort. Not that there is anything wrong with being a mechanic. But mechanics are generally not sources of in-depth technical knowledge in the biological sciences. I, for example, would not dream of telling Hemi how little he knows about cars. The same simple courtesy does not seem to be a part of the psyche of the anti-evolutionist.


All you could do to answer him is spit out "you're dishonest", "you quote mined". But the thing that got my attention is the mud hole you stepped in when you claim Pogge's predicted number of mutations that would be expected is a strawman, and yet at the same time you claim "yeah we see them".

Your conclusion is based on your inability to admit your own limitations in understanding the material and your devotion to the creationist cause. It would be possible to estimate a number of mutations accumulated within a certain time frame based on basic genetics and population genetics models. However, Pogge did not do this. His pseudo-estimate was premised, as I have repeatedly explained, on a naive interpretation of a statement.


Hemi's accusations and anger are typical of many lay creationists. Despite having a limited knowledge of the relevant issues, they have nonetheless convinced themselves of the 'certainty' of their position and therefore assume that anyone disagreeing with them, regardless of who they are or what they do for a living, must somehow be less informed, less intelligent, less capable then they are.

This sort of projection is common in such folk.

"Hemi", again...

Hemi at NAIG is afraid to comment here for some reason and has produced another silly post at NAIG. It is not worthy of any well thought-out reply, but I will address his silliest complaint. He also seems to think that I removed my other articles, apparently not realizing that by clicking on the blog title, you can get to the main page. Hemi's rant in blue.

So now you're saying that a list of observed altered traits
has nothing to do with phenotype or a list of mutations you can see in a species
is not part of it's phenotype?



Um, no, the phenotype IS the observed traits (more or less). Mutations do not always alter phenotype. In fact, most do not.


The last I heard any observable expression or manifestation
of any physical part of any life form was it's phenotype.

That is true. I wonder what the last you heard about "mutations" was? If you heard that all mutations alter phenotype, then you are just a typically disinformed creationist.


You claim "we can see these mutations", then you say you
can't see them.


As usual, the creationist distorts and misrepresents. You CAN 'see' the mutations - by comparing DNA sequence data. Pretty simple, really. But, as I have explained, not all mutations alter phenotype, you do not always (and usually do not) "see" the physical manifestation of them. I should have thought that someone suich as Hemi who has been involved in these 'debates' for at least several years might have picked up on at least the basics.


Pogge calcualted there would be about 20,000 mutations in
the last 4,000 years and you claimed that was a strawman, but you see the
mutations anyway, but it's the number that is a strawman
.

Yes, and I explained why. Perhaps the explanation was too 'technical'? Here, again - Pogge declared that this sentence:

"In some behavioral and cognitive traits, humans have changeddramatically since their evolutionary divergence from a common ancestor shared with chimpanzees. "

indicated to him (and only to him) that there was an "uneven split" in the distribution of mutations. It was this silly "interpretation" that lead to his concocted number. The number is, indeed, a strawman (or something very much like it). And yes, you can 'see' the mutations.


So I asked you for the ones you DO see, that was a strawman
too. Then you claim the mutations you see is not part of the phenotype. Unless
someone changed the definition of phenotype while I was working or something
they Are part of the phenotype if you can see them.

AGAIN, as I wrote, you can "SEE" the mutations. But a mutation does not mean an altered phenotype.


BTW, why did you take down Pogge's post and replace it with
the response I have on here? I don't wish to be on your goofy board.


I did not take down the article on Pogge's disinformation. You simply have not yet figured out how to click links, I guess. If you do not wish to be on my 'board', then perhaps you should not have chosen to comment on an article that I have on it.

Thursday, January 12, 2006

A response to "Hemi" on NAIG

I posted a link to this blog at the No Answers in Genesis discussion board, and "Hemi" (Tim Russell) responded to one of my articles here, there.

Rather than engage in a prolonged mud-fest over there, I thought I would deal with Hemi's comment here. Hemi's statements in blue:

So how many mutations do you predict would have occurred in the past 4,000 years? And seeing as how you claim above...

Quite simply - as far as mutations go, we should expect to see them in the
genomes of the specimens under investigation.We do.


Now all of a sudden it's a strawman to ask you to back up your claim?


I don't predict anything about exact numbers of mutations in a specific and arbitrary timeframe. Pogge does:

"If humans had 30 million mutations in 6 million years, and chimpanzees had 10 million mutations in 6 million years, then humans had an average of five mutations per year. In the last 4,000 years of recorded human history, there would have been about 20,000 mutations. Is there any evidence of that?"

Since Pogge's position is at best unwarranted and at worst a complete strawman, responding to it or anything drawn from it is a waste of time and effort.

I will say, however, that we would expect roughly an equal number of mutations to have occurred/accumulated in both the human and chimp genome in any particular time frame.

You didn't argue with Pogges number of predicted mutations in the past 4,000
years, you simply claim "we see them and to ask for verification is a strawman".

That is correct. There was no reason to argue with Pogge's numbers because they were premised on a strawman. Recall what he wrote -

"The first sentence seems to imply something more like a 30/10 split rather than a 20/20 split because "humans have changed dramatically" compared to chimpanzees."

The sentence implied no such thing. Pogge simply ran with his misinterpretation and set up the strawman. I am unsure why this is so difficult for you to grasp.


So instead of you claiming it's Pogge's ignorance or "purposeful deception",
just what is it you're doing? You claim you see the the predicted mutations,
then claim you shouldn't have to explain yourself.


No, I claim that we can see them - I should have remembered not to use such non-specific language as it is confusing for folks like you. Do I know which exact mutations occurred in any given time frame? No, and at this point in our technological ability, I do not think that this is possible in most cases. However, we can observe, if you will, a genetic distance between sequences which, in all cases I am familiar with, correlates with what we would expect under evolutionary constraints.

What are the changes to the human species these 20,000 mutations, or whatever number you say it should actually be based on your predictions, are observed? Eye color variations, skin color variations, maybe? Since it's a strawman for you to give a reference to these listed 20,000+- mutations you first claim you see, then ask "what mutations" can you at least give referencece to the list of the 20,000+- changes these mutations have caused in the human species in the past 4,000 years you claim we see?


No, again, the strawman is in concocting that number in the first place. Of course, it is only your unfamiliarity with genetics and biology in general that gives you the impetus to ask such a question. For if you had a basic understanding of these issues, you would realize that a mutation does not necessarily correlate to a particular change in phenotype. Asking for a list of altered traits, therefore, is premised on ignorance.

Wednesday, January 11, 2006

Pogge on Chimp-Human Differences

Ah, computer software guy David Pogge is up to his old tricks - mixing disinformation with insults and exposing his shallow grasp of science outside of his limited area of actual knowledge...
Well, grab a beer and your irony meter and let us take another gander into the mind of a creationist engineer-type. Again, as I could find no copyright information, I am reproducing the entire article here (without graphics).


This stellar essay can be found here. My comments in red.
===========================================


Feature Article - October 2005

by Do-While Jones [R. David Pogge]



Chimps Are Like Us

The chimpanzee genome has been decoded and compared to the human genome. What did scientists find? They found that the genomes are very similar! What a surprise!

*NOTE: In the original, Pogge had placed side-by-side a picture of a chimpanzee and Genie Scott, director of the National Center for Science Education. Nice fella, huh?

Every time a comparison of human DNA and chimpanzee DNA appears in the technical literature, we pass that information along to you. Our previous essays have been titled “98% Chimp”, “Monkey Business”, and “More Monkey Business”. Since those essays were written, the chimpanzee genome has been completely decoded.

*Um, no Mr.Pogge - the chimpanzee genome has been sequenced. That is not the same as having been decoded.


The September 1, 2005, issue of Nature was largely devoted to articles analyzing the similarities and differences in human and chimp DNA. The September 2 issue of Science contained an analysis of the September 1 Nature analysis.

In our previous essays, we described how different methods of comparison were used to produce different percentages. The calculated values were 98%, 98.5%, 98.8%, and 99.4%. What’s the “real” value? Well, it still depends on how you measure it.


*Very disingenuous of you, Mr.Pogge. As I pointed out previously, the values depend on what is being compared, not on 'how you measure it.' For example, it makes a difference if you are comparing genes to genes, or noncoding regions to noncoding regions. Both contain relevant yet
different information, as far as phylogeny goes.

… the draft sequence was announced but not formally published in 2003. Now the team, led by Robert Waterston of the University of Washington (UW), Seattle, confirms in Nature the oft-cited statistic that on average only 1.23% of nucleotide bases differ between chimps and humans. … The total genetic difference between humans and chimps, in terms of number of bases, sums to about 4% of the genome. That includes 35 million single base substitutions plus 5 million insertions or deletions (indels), says Waterston. 1

Four Percent Difference!

That’s right. Waterston says that the total difference is 4%, which somehow confirms the 1.23% average. We are still trying to figure out that math!


*Perhaps instead of ellipsing out the intervening paragraph, Mr.Pogge may have avoided his confusion:

"...on average only 1.23% of nucleotide bases differ between chimps and humans. But as suggested by earlier work on portions of the chimp genome, other kinds of genomic variation turn out to be at least as important as single nucleotide base changes. Insertions and deletions have dramatically changed the landscape of the human and chimp lineages since they diverged. Duplications of sequence "contribute more genetic difference between the two species--70 megabases of material--than do single base pair substitutions," notes Evan Eichler, also of UW, Seattle, who led a team analyzing the duplications. "It was a shocker, even to us." The total genetic difference between humans and chimps,..."


It really is not so hard to get, Mr.Pogge - providing, of course, you actually try.

See, the 1.23% difference refers to nucleotide-by-nuclotide comparions. That is, segment by segment compariosns. But what is one of the specimens is missing a segment? You cannot do a nucleotide by nuclotide assessment then, and the 4% figure takes into account these missing or
extra segments.
It is amazing how silly you can make your opponent look when you purposefully omit important information, isn't it Mr.Pogge?

If there really is only 1.23% average difference between human DNA and chimp DNA, how much average difference is there between two different human DNA molecules? Certainly it must be much much less than 1.23%. If that is true, how can DNA evidence be used in a court of law to convict criminals?

*According to the human genome project, any two differ by about 1 nucleotide per 1250 base pairs, or about 2.5 million, or about 0.08%.

How is DNA used in courts of law? Again, instead of feigning (exhibiting?) ignorance, Pogge could have done a simple internet search. Briefly, there are several ways to do this. One way is to extract DNA from a 'foreign' sample from the victim and digest it with enzymes. These enzymes will cut the DNA strands at specific areas. The 'cut' DNA fragments can then be separated by placing them in a gelatin like substance and running an electric current through the sample. The resulting ladder-like appearance of the gel can be compared to a similarly treated sample from the suspect. Because of the polymorphisms that exist, the fragments will run through the gel at different speeds. If the suspects fragments have run through the gel at the same speed as the sample from the victim did, then there is a match. Also, direct DNA sequencing can be performed, but this is probably time and cost prohibitive. Also, samples can be tested for the presence of certain alleles. Lots of ways to do this, but the first description is, as far as I know, the most common way of doing it.

Anyway, back to Pogge's question.

0.08% of 3.2 billion is, again, about 2.5 million. That is plenty to differentiate between individuals. What was the point of his question? That remains to be seen...


The papers confirm the astonishing molecular similarity between ourselves and chimpanzees. The average protein differs by only two amino acids, and 29% of proteins are identical. The work also reveals that a surprisingly large amount of genetic material--2.7% of the genomes--has been inserted or deleted since humans and chimps went their separate evolutionary ways 6 million years ago. 2


DNA contains the biological instructions for making proteins. If 29% of the proteins are identical, that means that 71% are different, doesn’t it? If the DNA is 96% the same, why are 71% of the proteins it produces different?

*Does Mr.Pogge really understand so little basic biology? Statistics?


Seriously, we’re just having fun with the numbers. Clearly human DNA and chimp DNA is very similar. We don’t dispute that.

*Oh, I see - he is just being silly...


But, as Mark Twain once said [actually it was Leonard Henry Courtney who said it], “There are three kinds of lies: Lies; damn lies; and statistics.” Scientists can present whatever numbers they want to emphasize whatever they want.

*So can anyone else, Mr.Pogge. Like you, for instance, in this essay in which you encourage creationists to "...point out the assumptions and impossible probability of enough of these mutations happening to create a new body plan or internal organ."

Of note, you do not say what the "impossible probability" is.

But the underhanded insult is not lost on me. And all scientists.


Which numbers are the most important is really a matter of opinion. Evolutionists always present the numbers in such a way as to diminish the difference between humans and chimpanzees to make it more plausible that they have a common ancestor.


*So, the insinuation is that we routinely distort the numbers - lie with statistics - to prove our point. Nice unsupported assertion, Mr.Pogge.


Similarity can either be the result of common ancestry or common design. The 96% (or whatever) similarity alone doesn’t prove common ancestry. It might be the result of a designer making two very similar things.


*Ah, this old chestnut. This reveals more about how much (little) Pogge understands about DNA comparisons than about the weak foundation of evolutionary conclusions. For it is the patterns of shared mutations which inform evolutionists of descent. The mere similarity is a byproduct of this. For example, look at this dataset alignment. The similarity is obvious, but it is the patterns of unique shared mutations that is most striking. I suspect that Pogge has never seen DNA sequence data, as has been the case with every creationist I have thus far encountered. So,
would a 'designer' put a 'broken' gene in both humans and chimps? Would a 'designer' put so many identical insertions is both?


If the similarity is the result of a common ancestor, then one must explain how the differences came about. Evolutionists typically claim the differences came from random mutations, filtered by natural selection. This argument sounded plausible before science discovered DNA, got a better understanding of genetics, and developed the concept of information theory. The evolutionary explanation was plausible before science discovered how many differences there are between species.


*In reality, the 'discovery' of DNA and our increasing understanding of what it does and how it operates has expanded not only legitimate science's understanding of evolution, but provided ever more evidence for it. Pogge is engaging what amounts to standard creationist Orwellian
propaganda.


It is our opinion that the important numbers are 35 million plus 5 million. That is, if you compare human DNA with chimp DNA, there are 35 million places where the molecules differ, and there are a total of 5 million places where the human DNA either has more or fewer bases than chimp DNA. (That is, there are 5 million places where bases have been “inserted” or “deleted” if one assumes that both kinds of DNA had a common evolutionary origin.) So, there are 40 million differences, total.

Who changed?

"It's frustrating that humans and chimps are so similar," says Andrew Clark of Cornell University in Ithaca, New York. It's difficult to tell whether a DNA sequence in humans that is missing in chimps was really added during human evolution or has simply been lost in the chimp lineage. 3


Remember that evolutionists believe (by faith)

*No, Mr.Pogge - your beliefs are based on faith (and this), our's are based on actual evidence.

that humans and chimpanzees both evolved from an unknown common ancestor about 6 million years ago. If evolutionary rates were the same for both humans and chimps, those 40 million base pair differences should be evenly divided between humans and chimps. In other words, our DNA would have about 20 million differences from the mythical common ancestor, and chimp DNA would have a different 20 million differences. Vain humans, though, would rather believe that the differences are split 30/10 (or 35/5) rather than 20/20 because we are so much more “dramatically” different from the apelike “common ancestor” than chimpanzees are.

*And? Was there supposed to be something of merit to consider here? Guess not...

In some behavioral and cognitive traits, humans have changed
dramatically since their evolutionary divergence from a common ancestor shared with chimpanzees. It seems reasonable to assume that a number of these changes were driven by positive Darwinian selection. However, although positive selection has been demonstrated for several human genes, the overall patterns of evolution of chimpanzee and human genes are consistent with selective neutrality. 4


There are two important points in this paragraph. The first sentence seems to imply something more like a 30/10 split rather than a 20/20 split because “humans have changed dramatically” compared to chimpanzees.

*Wow. That is quite a bizarre leap, even for Pogge. In reality, it implies just what it said - "In some behavioral and cognitive traits, humans have changed dramatically since their evolutionary divergence from a common ancestor shared with chimpanzees." Behavioral and
cognitive traits are housed where? Somebody help Mr.Pogge out - the brain. So, simple changes in the brain can account for these behavioral and cognitive changes. Another example of the shortcomings of pontificating on things you do not understand.


If humans had 30 million mutations in 6 million years, and chimpanzees had 10 million mutations in 6 million years, then humans had an average of five mutations per year. In the last 4,000 years of recorded human history, there would have been about 20,000 mutations. Is there any evidence of that?

*Why would there be evidence of a creationist strawman fallacy? Furthermore, what does Pogge expect to see? He, of course, does not say.


The more shocking statement in the paragraph quoted above is the one about natural selection. Evolution is supposed to work primarily thorough natural selection allowing positive changes to survive. But the nine authors of this peer-reviewed article think that most of the assumed changes in human DNA have no positive value. This makes natural selection an insignificant force in human evolution. If natural selection wasn’t the mechanism, what was?


*Ummm... Neutral evolution? Just like they said? Of course, they did not say that the changes had no positive value - they said most were neutral. I suggest that Mr.Pogge read up on some basic evolutionary theory and biology, as he continues making himself look like an underinformed propagandist.

Chimpanzees exist even though they don’t have the 40 million differences that humans have. So, those differences apparently aren’t necessary for survival. If creatures can survive with or without the differences, the changes are “neutral” as far as survival goes. But Darwin thought that “positive” differences, which promote survival, are the ones that drive evolution. That’s why some evolutionary scientists are looking for another method to explain evolution.


*Like who?


Looking for differences
Of course the primary reason for decoding the chimpanzee genome was to determine what differences make us “human.”

Perhaps we will learn how small differences in the code of life enabled us--but not chimpanzees--to cook soufflés, create symphonies, translate our own voyages into maps, build ever more complicated artifacts, and write plays that reflect the social intricacies of our lives. 5

Until now, genome sequence information has shown us how many seemingly very different organisms are amazingly like humans. At a conservative estimate we share about 88% of our genes with rodents and 60% with chickens. Applying a more liberal definition of similarity, up to 80% of the sea-squirt's genes are found in humans in some form. So it's no surprise that we are still asking, "What makes us human?" To apply genomics to this quest, we need to shift the focus to look at our closest living relative, the chimpanzee. Given that we share more than 98% of our DNA and almost all of our genes, chimps are the best starting point to study not the similarities, but the minute differences that set us apart. 6


The fact that one can fiddle with the numbers in such a way as to make the similarity between humans and sea squirts 80% is further proof that someone who is(conservatively) 88% rat can make the numbers say just about anything he wants.

*'Fiddle with the numbers'. Nice. Odd that a fellow that claims that 'science is against the theory of evolution' so frequently resorts to insults and distortions.

But we really don’t want to quibble too much about the numbers. The important thing is to examine the similarities and differences between humans and chimps.

Before we tell you what differences the study found, why don’t you try to guess? Of all the organs shared by humans and chimpanzees, which do you think is the most different? We’re going to go out on a limb and say that you probably think that the study shows the biggest difference between chimps and humans is in the brain. If so, you are really, really wrong.

Two major findings stand out. First, gene expression patterns differ less between humans and chimpanzees in the brain than in the other tissues
(bootstrap test, P < 0.0001). Second, the ratio of expression divergence between species to diversity within species is higher in testis than in any other tissue (5.6 versus 1.8 to 2.5, P < 0.0001). 7

So, they say, there is roughly three times more difference (5.6 to 1.8) in our testicles than in our brains. Let’s not go there!
[...]
Individual variations
When making comparisons of DNA sequences, we have to realize that there are limitations to the data.

… most of the chromosome 22 sequence has come from just one chimpanzee, it remains formally possible that some of the same polymorphisms also occur in chimp populations. 10

In other words, we know that there are differences in the DNA of different humans. The published human DNA genome is actually an average of several individuals. Each of those individuals differs by some percentage from the average. Unfortunately we have not been able to find out the actual percentage. In May, 2004, when the quote above was published, the DNA data came from only one chimp. We don’t know how many chimps were used in the genome that was published last month, nor do we know how much variation there is in the DNA of individual chimps. We are sure, however, that there is some variation. This diversity must certainly affect the 96% (or whatever percent) calculation.

But there is a more revealing statement about diversity in the most recent report.

Unfortunately, this pattern cannot be corroborated at the DNA sequence level because human DNA sequence diversity data collected in an unbiased way are not yet available. 11

What could this statement possibly mean? First, it seems to imply that results depend upon whose DNA is sequenced. If everyone’s DNA is exactly the same, it doesn’t matter whose DNA is used. But everyone’s DNA is somewhat different, and apparently it is different enough to affect the results. We don’t have a problem with this.


*Perhaps not. But it does appear that you have a problem with context. For the previous sentence sheds some light on that quote:

"Thus, the higher ratio of gene expression divergence to diversity in testis as compared with the other tissues is indeed indicative of positive selection. Unfortunately..."


The disturbing phrase is “data collected in an unbiased way.” That implies that there is a way to collect data that would be biased to make the difference between humans and chimps appear more (or less) than it actually is; and that the biased method was the one that was used. So, we ask ourselves, “How could one bias the data?”


*Actually, Mr.Pogge, in science, 'bias' does not always mean what you think, and it certainly has nothing to do with what you imply. Again, Mr.Pogge's real problem is with context and comprehension:

"However, because realistic evolutionary models for neutral expression changes are not yet available and because environmental factors have a considerable influence on gene expression diversity, a high ratio of divergence to diversity represents an indication rather than proof of positive selection. As seen above, testis differs from other organs studied in that the ratio of expression divergence to diversity is higher (Fig. 1). If the cellular composition of testicles differed between humans and chimpanzees more than it does for other tissues, this observation could be explained by only a few genetic differences between the species. However, although human and chimpanzee testicles differ in size, there is no evidence that the cellular composition of this organ differs between the species (29). Another possibility is that the genetic component of the expression diversity in testis is not lower than expected from the expression divergence, but that gene expression patterns in testis have a smaller environmental (i.e., nongenetic) component. In that case, we would expect genes expressed in testis to be subject to as much constraint as genes expressed in tissues such as liver or heart that have a comparable expression divergence. The property of being expressed in testis should then have a similar effect on diversity levels in other tissues as the property of being expressed in, for example, liver. However, we find that among the five tissues, expression in testis is associated with the highest number of significant reductions in diversity in tissues other than testis, whereas expression in liver is associated with the highest number of significant increases of diversity in tissues other than liver (fig. S3) (15). This suggests that strong selective constraints on genes, rather than low environmental influence, account for the low extent of expression diversity in testis. Thus, the higher ratio of gene expression divergence to diversity in testis as compared with the other tissues is indeed indicative of positive selection. Unfortunately, this pattern cannot be corroborated at the DNA sequence level because human DNA sequence diversity data collected in an unbiased way are not yet available. However, we can test predictions about the chromosomal distribution of instances of positive selection in genes active in testis."

Emphasis mine. What a mouthfull... But, as one can see, the 'bias' mentioned has absolutely nothing to do with trying to get the numbers to support human-chimp ancestry as Pogge so dishonestly (or incompetently?) indicates. It has to do with examining the effects of environment versus positive selection. As far as the actual phrase used ("...because human DNA sequence diversity data collected in an unbiased way are not yet available.), this website will likely have the answers, and from a quick reading of it, I suspect that the paper's authors are referring to the fact that sequence data are not available for
representatives from all human populations, and therefore, the data available are "biased" in that they come from a limited number of populations.

If one believes in evolution, and believes that some people have evolved farther from apes than other people, what would that imply about differences in DNA? Are the results unfairly biased because of the color of the skin of the people who supplied the samples? Surely, they don’t mean that! But if they don’t mean that, what do they mean?

*Who would have thunk it? Pogge is now implying racism? What is next? Are all evolutionists Nazis, too Mr.Pogge? Or will that be saved for another of your brilliantly insightful essays?

What have we learned?
We could have told you what “scientists say” at the beginning of this essay; but if we had told you their conclusion right up front, there would have been no point in reading what we have to say. Here is what McConkey and Varki have concluded:

Can we now provide a DNA-based answer to the fascinating and fundamental question, "What makes us human?" Not at all! Comparison of the human and chimpanzee genomes has not yet offered any major insights into the genetic elements that underlie bipedal locomotion, a big brain, linguistic abilities, elaborated abstract thought, or any other unique aspect of the human phenome. 12

In all fairness, we need to say that the rest of the article we quoted above was a shameless plea for more money for research. One could argue that effective fundraisers never say, “We’ve got all the answers, now give us more money.” But that argument would rest on the assumption that scientists cast truth aside and say whatever they have to say to get more funding. Perish the thought! If one can’t believe what scientists say, what can one believe? But it isn’t just McConkey and Varki who have said that scientists haven’t found the answer yet.

Scientists produced a rough draft of the chimpanzee DNA sequence, and aligned it with the human one, and made an intimate comparison of the chimp and human genomes. "It's wonderful to have the chimp genome," says geneticist Mark Adams of Case Western Reserve University in Cleveland, Ohio, who was not on the papers. "It's the raw material ... to figure out what makes us unique."

But those hoping for an immediate answer to the question of human uniqueness will be disappointed. "We cannot see in this why we are phenotypically so different from the chimps," says Svante Pääbo of the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany, a co-author on one Nature paper and leader of a study in Science comparing gene expression in chimps and humans. 13

We still know what we always knew. Specifically, chimps look and act like humans more than other animals. Chimps’ DNA and internal organs (excluding one pair of external organs ) are very much like ours. But there is still no way to tell if that similarity is the result of descent from a common ancestor, or creation by a common designer.

*What an absurd, naive, position.

When I was in graduate school, not knowing exactly what I wanted to do, I decided to do a rotation in a lab that looked at DNA sequence data to study evolution. I had never heard of such a thing, but it interested me (in part because I did not want to do animal research). I remember the first time I saw a DNA alignment. It hit me hard. The patterns were so obvious. The simplicity of the rationale for using DNA sequence data - not to mention the fact that it has been tested - made it all so clear. Mutations happen. Sometimes, they get passed on to offspring. Over time, the patterns of these unique shared mutations can be used to infer descent. It is not faith. It is not speculation. It is testable and repeatable science. It is common sense. No 'common
designer' is needed to explain the patterns, only simple heredity.



CONCLUSION:


Pogge again relies on a shallow grasp of the information - that or is quite dishonest in his treatment of it. He uses out of context quotes and ridiculous extrapolations. He uses thinly veiled insults and puts words (thoughts) into the mouths of actual scientists.

Another example of dishonest propaganda from scienceagainstevolution.org and R. David Pogge.

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