Evidence against evolution - part 10000000.....

DaveScot at uncommondescent (Nov 28th) thinks he has found some compelling evidence against evolution. Under the headline "The sound of a nested hierarchy shattering" he writes:

Chromosomal sex determination in the platypus discovered to be a
combination of mammal and bird systems. The resemblance to birds is now more
than just superficial.

http://www.newscientist.com/article.ns?id=dn6568

From this he seems to want to claim that there is a problem with the idea of common descent. Why? I have no idea. DaveScot, how about this for possible explanation: birds and mammals shared a common ancestor and modern mammals retained certain genes, modern birds retained some other genes and the platypus retained a combination of genes. Why not? Mammals diverged from birds 300 million years ago and montremes diverged from other mammals 150 million years ago.

How desperate do IDists have to get?

Edit: a couple of comments were added to the above thread, and I felt compelled to address these as well.

"J" adds a list of five reasons under the headline "Refutation of the Dinosaurian Origin of Birds" from Mayr's "What evolution is" and "Jehu" responds with "What? Ernst Mayr doesn’t believe birds evolved from dinosaurs? ". "J" and "Jehu" are doing the old wedge strategy where "if scientists are not in complete agreement over something, then science is wrong" argument. In this case, the impression one is left with is that either birds evolved from dinosaurs OR evolution is wrong.

But , the reason that list was in Mayr's book was because there has been a debate whether birds evolved from archosaurian reptiles or from theropod dinosaurs. Scientists supporting the reptile connection supplied the list as evidence for their position. "J" and "Jehu" of course want to see this as some form of confirmation that evolution is in trouble, when it in fact is just part of the normal scientific process. In fact, more recent evidence has shed light on the debate and in a National Geographic interview, Mayr stated:

Archaeopteryx, therefore, is closely related to the theropods. This in turn means that theropod dinosaurs are the ancestors of the modern birds that followed Archaeopteryx.
The find, according to Mayr, "not only provides further evidence for the theropod ancestry of birds, but it blurs the distinction between basal [the earliest] birds and basal deinonychosaurs," their fearsome-clawed ancestors.
"I do think that the question of a theropod
ancestry of birds can now be considered settled once and forever," Mayr said.

So, there you go. The evidence does seem to point to a dino-bird connection.

One last point, and though it might seem minor, I think it is actually quite important. After detailing the five objections mentioned, "J" states the reference as: (Ernst Mayr, What Evolution Is: Now Everyone Please Stop With This Dinosaurs-Became-Birds Nonsense. (2001), p. 68.). The "Now Everyone Please Stop With This Dinosaurs-Became-Birds Nonsense" is NOT in Mayr's book. "J" made that up. It is NOT there. "J" effectively told a LIE. (All in the name of the wedge, no doubt).

Again, How desperate do IDists have to get?

Massmurder will occur

I'm not particularly interested in advocating atheism but sometimes, like after reading the thread that GilDodgen at uncommondescent started (22nd Nov, with it's following comments), I feel the need to. The discussion starts out fine enough, but quickly degenerates into a "if there is (or if people believe there is) no absolute morality then people will kill eachother indiscriminately" kind of argument (as argued by for example DaveScot). I'm not going to write an exhaustive rebuttal to this, but instead just supply some points for you to consider.

1. Isn't this a rather grim view of humanity? Whether you are christian, muslim, buddhist, atheist or jedi, think about it. Are we to believe DaveScot and friends when they say that the only reason we don't kill indiscriminately is because we know someone is watching our every move and has the capacity to severely punish us? The reason you don't kill that annoying workmate, person at school or guy on the cellphone is hardly because you think that you will burn in hell for it. You don't do it, for the simple reason that you KNOW that it is wrong (or more likely, perhaps, it never even occurred to you). Whether or not that knowledge is based on something supernatural or is a result of evolutionary forces (and/or lots of other possbilities) hardly matters. DaveScot's friends would have us believe that only the threat of severe punishment deters murder. That's the reason sociopaths don't do more bad things than they do. The rest of us just don't do them.

2. If you compare theory (atheism->evil) to reality, an interesting picture emerges. In the US, around 75% of the total population is christian. Around 75% of the prison population is also christian. No surprises there. In the US, around 3-8% (depending on source) of the population describe themselves as atheists. Around 0.2% of the prison population also describe themselves as atheists. It would actually seem like atheists are LESS likely to indulge in criminal behaviour. Why would that be? You can always argue that maybe atheists are less likely to go to prison because they are less likely to get convicted (you can even insert your favorite conspiracy theory to account for this, if you wish). You can argue that atheists commit more serious crimes (but if you do, you'd better back that up with some data). You could argue all sorts of things - maybe even the thought that atheists simply are NOT evil and that atheism does not lead to bad behaviour. Do you reckon we would ever find DaveScot et al doing that?

Michael Behe and astrology

In the Dover trials, where intelligent design was found not to be science, ID proponent Michael Behe stated that astrology could be considered science under his definition of it. It now seems that Michael wants to clarify what he actually meant.

From deposition statement:

17 Q. Using your definition of theory, is Creationism -- using
18 your definition of scientific theory, is Creationism a
19 scientific theory?
20 Behe. No.
21 Q. What about creation science?
22 Behe. No.
23 Q. Is astrology a theory under that definition?
24 Behe. Is astrology? It could be, yes.

Michael Behe clarifies:

I was not thinking of the modern superstition of astrology, but of the idea of astrology in the middle ages, when people were trying to discern what forces actually were in play in nature.
...
...
No, not modern astrology, as practiced by card readers with bandanas on their heads and such. I had in mind astrology of centuries ago, when educated people thought it might really have explanatory power.

Are we to believe that Behe considers something science just because it was considered science centuries ago. Let's give him the benefit of the doubt and examine that claim by looking at the court transcript from above. There, Behe claims that creationism is not science. But, centuries ago when astrology was considered science, creationism was also considered science (in the sense than "people were trying to discern what forces actually were in play in nature. "). So, logically, creationism should also be considered science (at least, that is what he should have said in the trials - or he should have said that neither were). The fact that he didn't speaks volumes.

The Behe crowd are now eager to point out that Behe does not support astrology. They claim that more careful reading of the court transcripts not only show that not only does he does not support astrology, he never meant that modern astrology is to be considered science in the first place. In the trials, Behe stated:

Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences.There are many things throughout the history of science which we now think to be incorrect which nonetheless would fit that -- which would fit that definition. Yes, astrology is in fact one, and so is the ether theory of the propagation of light, and many other -- many other theories as well.
...
...
Nonetheless, we can't go back and say that because they were incorrect they were not theories. So many many things that we now realized to be incorrect, incorrect theories, are nonetheless theories.

Discarded scientific theories are, as Michael points out still theories. But, modern science would not call these old astrology theories scientific in the first place, while under Behe's definition they actually would be. And this opens up a whole can of worms. The thrust of the questions asked to Michael was not whether or not he believes in astrology - it's in the type of research that is considered valid under his definition. Astrology would be. And presumably ghost-hunting, Reiki and faith-healing as well.

Reconsider your scientific ideas - part 2

Not content with criticizing "Darwinists"for not challenging their ideas enough (see my blog from Nov 15th) , ID followers also LOVE to point out when scientists do so. Paul Nelson at Id the Future
does just that:

A friend who works at a national biomedical facility told me recently that he now finds it impossible to keep up with all the scientific literature challenging neo-Darwinism (i.e., textbook evolutionary theory). "The stuff just piles up in my office," he said. "I glance at the abstracts, download the pdfs, but can't read it all." We agreed that during 2005-2006, while the intelligent design controversy has been soaking up headlines and media scrutiny, leading evolutionary theoreticians themselves have been quietly uttering heresy in the halls of Darwin. It's easier to misbehave, you know, when someone else (ID) is really acting up and drawing off all the attention.

So not only do scientists sometimes challenge Darwinism, they do it all the time. Evolutionists - you're damned if you do and damned if you don't!

IDers see it as a weakness when scientific theories (well, the ones that deal with evolution, anyway) are questioned, which is a very interesting viewpoint considering that it is a big part of what science actually is all about. It has nothing to do with heresy as Paul states, but is merely part of the scientific process. But he is right about one thing - ID is acting up. Design interference is what I call that.

Reconsider your scientific ideas

GilDodgen at uncommondescent blogged on Nov 15th, 2006 about how the Stardust mission had collected data making scientists rewrite "the text on how the solar system formed". He then asks:

If, in a hard science like this, previous assumptions can be reexamined and even overturned, how about the assumptions of a soft, philosophical “science” like Darwinism?

GilDodgen is obviously trying to get "Darwinists"to reconsider naturalistic evolution and start embracing intelligent design. But his argument is extremely silly. The only way he can make it work is if the "Stardust scientists" concluded (or at least examined the possibility) that the solar system formed due to the influence of an intelligent designer. That's hardly the case.

Peer review sucks?

Denyse O'Leary, the ever championing ID journalist, has been criticizing peer review in a series of articles. I would like to give some comments regarding one of these.

Writes she:
Peer review problems went "public" mainly as a result of recent high-profile scandals like Science's peer-reviewed Korean stem cell research paper that turned out be fraudulent.
...
Some argue that the peer review system was designed to detect incompetence but not fraud. Flawed, yes, but fraud, no.
...

Yep. It's true. Published research can be both fradulent and flawed. There is a certain level of honesty and competency expected and it is not always met. The question, then is, what do we do about it? You can't really just moan about something unless you have a better alternative. Denyse offers two:

1) Interestingly, the ID journal, Progress in Complexity, Information, and Design (PCID) has opted to return to the early twentieth century approach, where a senior scholar recommends a junior scholar for publication. Time will tell if this old method can be revived successfully.

I totally fail to see why this would solve any problems. Instead of having several peer reviewers, you now have one. Why would this person be any less likely to be fooled by frauds and incompetents?

2) Internet-based technologies may enable a more open and dynamic system. In a way, it can be compared to the blogosphere. The blogosphere, for all its faults, has been a breath of fresh air in media. It has restored the original concept of news as what people want to hear about rather than what gatekeepers think they should want to hear about.

I actually think that this is an idea that might have some merit, but not in the incarnation that Denyse imagines. Her version would essentially turn published research into Wikipedia where anyone can write whatever they want about anything. Yes, the "winning" concept would be the one where people get what they want to hear about. So, are we then really supposed to let the whims of public opinion decide what is valid research. I'm sure that IDers, homeopaths and astrologers would love it. Denyse, there has to be some "gate keeping" done.

So, two alternatives are offerered and none of them seem to offer any improvements. Oh, well. Back to the drawing board.

I just want to comment about one thing more that Denyse writes in her article:

Soothing comparisons have frequently been made to Winston Churchill's characterization of democracy as the worst system - except for all the others. But the convenient analogy to democracy fails. In the first place, the secrecy in which peer review operates make it a poor analogue to democracy. Second, democracy aims primarily to give every citizen a vote. The fact that some citizens vote for cranks or criminals does not mean that democracy has failed.

I suspect that Denyse has misunderstood why this so-called comparison has been made. Peer review is not analogous to democracy as she implies that scientists see it. The point of the "comparison" is just to point out that out of a variety of bad choices, peer review is the best (although this is debatable). All she has done here is to build and attack a strawman.

ID predicts...

While browsing the web, I can across the IDEA Center website. It claims:

FAQ: Does intelligent design make predictions? Is it testable?

The Short Answer: Yes. Intelligent design theory predicts:
(1) High information content machine-like irreducibly complex structures will be found.
(2) Forms will be found in the fossil record that appear suddenly and without any precursors.
(3) Genes and functional parts will be re-used in different unrelated organisms.
(4) The genetic code will NOT contain much discarded genetic baggage code or functionless "junk DNA".
Each of these predictions may be tested--and have been confirmed through testing!

First of all, intelligent design did NOT predict any of these. All the observations made above were done before ID was ever proposed. Also, ID predicts the above four points as much as it predicts the four below:
(A) High information content machine-like irreducibly complex structures will NOT be found.
(B) Forms will be found in the fossil record that appear SLOWLY and with precursors.
(C) Genes and functional parts will NOT be re-used in different unrelated organisms.
(D) The genetic code WILL contain much discarded genetic baggage code or functionless "junk DNA".

These four points (A-D) are the opposite of 1-4, yet they are still in accordance with ID. You could, in fact, make any observation and it would be in accordance with ID. Is this bad you might say(?). It sure is. Can you imagine if someone claimed that (s)he could predict next weeks winning lotto numbers and as evidence (s)he presents all combinations of numbers possible. For sure, one of those combinations will win, but you would hardly claim that the "predictor" actually predicted it, would you?

Surprised Darwinists

PaV at UncommonDescent blogged on 6th Nov, 2006

Darwinists are Always Surprised

by PaV on November 6th, 2006 · 32 Comments

Here’s a study on E. Coli. They force the bacteria to “mutate” to process glycerol. After six days, sure enough, a kinase shows up to handle the glycerol. But what is a “surprise” is that RNA polymerase shows up besides. It seems that two simultaneous mutations took place. But, of course, this is ONLY a surprise if you think RM+NS brought it about.

The authors say:

Mutations also appeared in a second, unrelated gene for an enzyme called RNA polymerase. “That was a surprise to almost everybody because RNA polymerase is involved in one of the core processes of any cell,” said Palsson. “You wouldn’t expect that gene to change because a wide variety of cellular process would be affected; it’s like replacing the wiring system in a building when a light bulb burns out. But we repeated the experiment more than 50 times and mutations in the RNA polymerase gene appeared again and again.”

I also enjoy the hesitation you almost hear as the reporter has to backtrack somewhat from RM+NS (listen for the word “presumably”):

All the mutants arose in the experiments presumably as the result of naturally occurring errors in copying DNA into daughter cells during cell division.

We here at UD have a better idea about what’s going on.

The reason that it came as a surprise was not because of the occurence of two mutations, but rather (as PaV points out) because one of them was in the RNA polymerase gene, which you would think would be irrelevant for the new function acquired. Obviously it wasn't, so SURPRISE!!

PaV claim that the people at UncommonDescent have a better idea. That probably involves something along the lines of the mutations not being random but that the organism actually sensed that it needed these mutations (as he argued in this thread). I have two things to say about that:
1. Given that, in this experiment, one in roughly 100 billion of all organisms actually get the selected for mutation(s), the notion that the organisms actually sensed that they needed it seems, if not far-fetched then at least like they were REALLY crap at sensing.
2. Even is the organism sensed that it needed to mutate RNA polymerase, it would still come as a surprise since it is not something that was expected.

PaV continues:
By the way, some time back, in a heated debate over bacterial mutation and point mutations, I calculated that the amount of bacteria needed to provide TWO simultaneous point mutations simply through random chance would be so large that the known universe couldn’t contain it. I’m sure my calculation was off somewhere, but I think you get the picture: two genes being affected simultaneously is something that cannot happen by chance alone.

You can read that thread (posted 5th Sept, 2006 under the heading How random is random mutation?) for yourself. PaV ended up backing out since his calculations more than just "off somewhere". So given that he brings this up again SURPRISES me, but maybe he hasn't learned from his mistakes.

Darwin is the father of fascism?

O'Leary at Post-Darwinist is fond of slandering evolution. In this blog of hers from 6th Nov 2006 she quotes A. N. Wilson who in Telegraph's World of Books wrote:

"Darwin, the product of British imperialism, was surely the father, among
other things, of European fascism."

There are many definitions of fascism, but they mostly include the presence of a dictator, no allowance of opposition, strict social control and that the "primary guiding principle that the state or nation is the highest priority, rather than personal or individual freedoms". This hardly sounds like Darwin (or evolutionary science by extension). The dictator sounds more like a vile intelligent designer to me...

Dolphins sprout legs?

Uncommondescent blogged about the find of a dolphin that had an extra set of fins.

From above article:
Japanese researchers said Sunday that a bottlenose dolphin captured last month has an extra set of fins that could be the remains of hind legs, a discovery that may provide further evidence that ocean-dwelling mammals once lived on land.

Some Uncommondescent commenters seem to be stuck on the idea that since these fins look like fins and not legs, the researchers should not claim that this provides "further evidence that ocean-dwelling mammals once lived on land". Let's examine this reasoning. Science has come to the conclusion that the ancestors of dolphins (and whales in general) were once land-dwelling tetrapods (i.e. they had four limbs). For these ancestors to evolve into dolphins, they must obviously have lost their legs somewhere along the way. This is not likely to have happened in one generation!!! More likely, the process would have been fairly gradual, starting with a four footed animal changing into a four-finned animal that subsequently lost it's rear fins - leaving us with the dolphins we see today. So, if today, a dolphin was found that sported extra rear limbs, we would hardly expect these to look like legs any more than we would expect it's front limbs to do. What we would expect, if descent with modification is true, is that these limbs would look like fins. The extra limbs found on this dolphin is thus consistent with the view that dolphins evolved from land-dwelling mammals.

JasonTheGreek asked at Uncommondescent: "Based on the fins, is there any way to show these were likely actual legs? Could these legs have held the weight of the body? ". The answer is no to both questions. When the pathway leading to the expression of these fins was last active, it was making fins, not legs. (Of, course, whether or not the extra pair of fins provide evidence that the ancestors of dolphins once lived on land depends on if they are due to an evolutionary remnant being switched back on - something that is by no means certain).

So, this find is consistent with dolphins have land-dwelling ancestors. However, like any singular piece of evidence, it is not a nail-in-the-coffin either for or against the theory. It is just a piece of evidence added to an already large pile of evidence that supports evolutionary theory.

Designers are impossible?

This article was inspired an article on IdTheFuture by Paul Nelson that was rebutting some comments Richard Dawkins had made. This article is, in essence, a rebuttal of that rebuttal.

Dawkins wrote:
Given that chance is ruled out for sufficient levels of improbability, we know of only two processes that can generate specified improbability. They are intelligent design and natural selection, and only the latter is capable of serving as an ultimate explanation. It generates specified improbability from a starting point of great simplicity. Intelligent design can't do that, because the designer must itself be an entity at an extremely high level of specified improbability. Whereas the specification of the Boeing 747 is that it must be able to fly, the specification of "intelligent designer" is that it must be able to design. And intelligent design cannot be the ultimate explanation for anything, for it begs the question of its own origin.

Paul Nelson wrote:
Michael Ruse muttered to me darkly several years ago that Dawkins seems not to understand that this argument makes evolution by natural selection true by necessity -- hardly a happy position for any putatively empirical theory to be in.

Paul uses the analogy of a basketball game where it is only possible for the home team to win. The outcome of the game has been settled a prioi and the visiting team will loose even if they score the most points. But Paul is wrong; Dawkins argument does not make evolution true by necessity. Dawkins states above that "we KNOW of only two processes..." (emphasis added) and he then chooses one of the two KNOWN ones. What Dawkins (and most scientifically literate people) understand is that there could be more UNKNOWN processes. Future research might shed some light on these, but until that time, there is NO reason to consider any of them. If Paul's basketball analogy was to be correct, it should read something like: The home team has scored the most points and is therefore leading the game. However, other teams might join the game and it is possible that the home team will loose then (which doesn't make for a good analogy, really).

This hardly leaves evolutionary theory in an unhappy position.

Paul Nelson wrote:
When a philosopher hears that a theory about questions of empirical fact cannot be false, or that its competitors cannot be true, his tracking radar turns on. He also quotes NYU philosopher Thomas Nagel:

But God, whatever he may be, is not a complex physical inhabitant of the natural world. The explanation of his existence as a chance concatenation of atoms is not a possibility for which we must find an alternative, because that is not what anybody means by God. If the God hypothesis makes sense at all, it offers a different kind of explanation from those of physical science: purpose or intention of a mind without a body, capable nevertheless of creating and forming the entire physical world. The
point of the hypothesis is to claim that not all explanation is physical, and that there is a mental, purposive, or intentional explanation more fundamental than the basic laws of physics, because it explains even them.

Paul is possibly confused about what actually is true and what we can know scientifically to be "true". The two are not necessarily the same. There might, indeed, be a God as presented by Nagel, but since we have no empirical knowledge about it (and more to point probably never can), why should we even consider it? Some philosophers and religious people obviously do, but their resoning is not based on evidence and is from a scientific perspective, therefore, meaningless. So, Paul, it is not that some competitors can't be true, it's just that from a scientific viewpoint, some of them don't stack up.

Paul Nelson quotes Thomas Nagel again:
All explanations come to an end somewhere. The real opposition between Dawkins's physicalist naturalism and the God hypothesis is a disagreement over whether this end point is physical, extensional, and purposeless, or mental, intentional, and purposive. On either view, the ultimate explanation is not itself explained. The God hypothesis does not explain the existence of God, and naturalistic physicalism does not explain the laws of physics.

Apart from the fact that I'm not sure what naturalistic physicalism is (I've equivalated it with methodological naturalism), I have only one thing to say. If there is no way (as Nagel seems to imply) to know "the ultimate cause", why not just say "I don't know", instead of just making things up?