Wednesday, 30 January 2013

Common Descent Part 3

Arguments Against

When looking at creationist web sites for arguments against common descent, the first thing that becomes apparent is that creationists conflate common descent with evolution. For example, from here:
Common Descent (Darwinism)–Science or Pseudoscience?
REVIEW HOW COMMON DESCENT (MACROEVOLUTION) HOLDS UP WHEN USING THE SCIENTIFIC METHOD OF TESTING AN HYPOTHESIS
As far as these people are concerned, common descent, macroevolution and Darwinism all mean the same thing! Also here:

Several of the criteria said to distinguish the scientific status of naturalistic evolutionary theories (hereafter "descent") from admittedly nonnaturalistic theories of creation or design (hereafter "design") will be examined.


This example was written by a philospher of science (Stephen Meyer), who really should know better. But, then again, he is a creationist...

Many of the arguments presented against common descent are really arguments against something else, such as abiogenesis. I am not going to discuss them here.

Uncertainty in the Tree of Life


A common argument is that scientists disagree on how organisms are related, or they change their minds about where the organism should be placed in the tree of life. Why this counts as evidence against common descent is beyond me. It is like deciding that the Roman Empire never existed because historians have uncovered new evidence that changes the accepted date of birth of one Roman emperor.

Gaps in the Fossil Record

Another argument is that there are gaps in the fossil record. Fossilisation is very rare, and the amount of ground dug up is tiny (think about how much of the land around your home has been excavated for fossils). In fact, on the basis of common descent, Darwin predicted that a transitional between reptiles and birds would be discovered, and indeed, before his death, the fossil of archaeopteryx was discovered. Of course, many creationists refuse to admit archaeopteryx is a transitional, insisting it is a reptile; the rest refuse to admit it is a transitional, and insist it is a bird. Such is the creationist way of dealing with transitionals.

This argument is becoming ever more silly as more transitional fossils are appearing. See here for some articles at Panda's Thumb on that:
http://pandasthumb.org/archives/evolution/transitional-fossils/

Here is a great example of Duane Gish's deceptions about triceratops being exposed:
http://ncseweb.org/cej/3/3/dilemma-horned-dinosaurs

Common Design

Creationists and IDists often put up "common design" as a viable alternative to common descent. According to the common design hypothesis, all mammals share the same features because they were designed to be similar, just as all cars share a bunch of similar features, while aeroplanes share a different set of features.

At first glance, this seems quite reasonable, but scratch below the surface, and it all looks a bit dodgy. Things that are really designed, like cars and aeroplanes, share a lot of common features, and those features do not follow the same pattern as common descent. Modern cars and aeroplanes use microprocessors, but 60 years ago neither did. The design of cars and aeroplanes does not form a nested hierarchy. New technology is added to both cars and aeroplanes. In contrast, new "designs" in evolution appear only sporadically.

Chimeras


The chimera was a creature from Greek mythology, part goat, part lion and part snake. However, the term has come to be used more generally to mean a creature made up of part of other creatures. Surely the "common design" hypothesis would lead us to expect such chimeras?

Answers in Genesis give their reason why we see no chimeras. However, the important point here is that common descent predicts there will be no chimeras. Common design does not; it merely rationalises the fact after the event.
http://www.answersingenesis.org/tj/v16/i1/chimeras.asp

Summary


To my mind the evidence for common descent is conclusive. There is just too much of it out there and it fits together too well. In all my discussions with IDists and creationists, the only real argument against it I have come across is that the Bible says otherwise. Nevertheless, most Christians do accept common descent.

By the way, there is a strange phenomenun on discussion boards with IDists; if you are arguing about common descent, the IDists who accept common descent are strangely quiet. Why is that, I wonder?

Monday, 21 January 2013

Common Descent Part 2

What Does Common Descent Explain?

A scientific claim needs to make testable predictions, but it also needs to be useful, to help explain the world we see.

The Distribution of Eyes

There are various sorts of eyes in the natural world, such as the compound eye of the insect, the camera eye of vertebrates eye and the alternative camera eye of octopi and squids. According to common descent, the eyes that a creature gets depends on their ancestry. If you are descended from the first organism to evolve a rudimentary compound eye, you get a compound eye. Thus, while fish and squid live in the same environments, fish have retinas wired one way, squid have retina wired the other. One is, presumably, better in that environment, but who gets what is determined by their evolutionary history, not their current needs.

See here:
http://scienceblogs.com/pharyngula/2006/11/the_eye_as_a_contingent_divers.php

Creationists sometimes say that the designer equipped each "kind" with the eye most suited to its environment. The squid, the shark and the whale "kinds" need eyes that work well in water, so we would predict them to have the same eyes. Advocates of common design might argue that one type of eye is advantages in a more specific niche, perhaps for predators at great depths. That is a reasonable argument, as long as they follow it though. The creationist scientist should be able to state what niches a certain eye type is best suited for; not just the two camera eyes, but the compound eye and all other eyes. He should be able to give some reasoning as to why the eye works best in that niche. And then he can show how the "kinds" in that niche (or at least originally in that niche when created) have the optimum eyes.

As far as I am aware, no one has ever attempted that. Why not? Because creationist scientists know that creation science fails the prediction.

Vitamin C Pseudogene

Most mammals can synthesise their own vitamin C, so cats, for instance, survive very well on a diet that excludes fruit. This is not true of humans, and two centuries ago sailors would regularly die a very painful death of scurvy (over half the crew might die on a long voyage). Curiously, humans do have the gene that codes for vitamin C synthesis, but it is broken (it is therefore described as a pseudogene). This same pseudogene has been found in chimpanzees, orangutans, and macaques, as well as guinea pigs. The common descent explanation is that a common ancestor of humans, chimpanzees, orangutans, and macaques had a mutation that destroyed the functionality of the gene, but as this ancestor ate so much fruit, it made no odds to the ancestor, and spread through the species. Thus today, all four species have the same error in the pseudogene (and this happened independantly for the guinea pig).

More here:
http://members.iinet.net.au/~sejones/cmnctsry.html#vtmncpsdgn

How does creationism explain this?

Vestigialism

Certain features can be identified as having a primary use in one species and not in another. The wings of an ostrich are useless for flying, but are clearly still wings. Sure, they have some other purpose, but not a purpose you need wings for. The cassowary has virtually nothing in the ways of wings, not enough to be useful for anything - but there is something there still. Some cave dwelling animals have the vestiges of eyes, but skin grows over them, preventing light, should there be any, from actually getting to the eye.

Common descent says that in the ancestor, these were fully functional features - the ancestor of the ostrich could fly, the ancestors of the cave dwellers lived on the surface, and found the eyes to be useful. The modern organism lives in an environment or manner that makes the feature useless, but it still remains.

Atavism


Occasionally humans are born with tails, whales and snakes with legs. Common descent says this is a throw back to our respective ancestors. If humans were created without tails, where do these tails come from?

More..

There is plenty more evidence, and much of it is presented on Talk.Origins. The interested reader may like to read this exchange between Talk.Origins and True.Origins:

http://www.talkorigins.org/faqs/comdesc/
http://www.trueorigin.org/theobald1a.asp
http://www.talkorigins.org/faqs/comdesc/camp.html
http://www.trueorigin.org/ca_ac_01.asp

Here are other interesting sites:
http://home.planet.nl/~gkorthof/korthof84.htm
http://members.iinet.net.au/~sejones/cmnctsry.html

Wednesday, 16 January 2013

Common Descent Part 1

Pretty much everyone accepts some degree of common descent; creationists generally believe that all canines (the dog "kind") evolved from a single species. However, I am talking here about universal common descent, the claim that all living things are related, and are descended from a common ancestor. When I say common descent on this blog, I mean universal common descent, rather than limited common descent.

Let me say up front that there are issues in science revolving around that common ancestor. It may be that there was actually a whole bunch of ancestors that appeared independently, and subsequently exchanged genes. It was a very long time ago, and the evidence available today is scant. So the argument can be summarised as the claim by mainstream science that humans and (say) bananas share a common ancestor, and the claim by creations that they do not (and indeed, usually that even humans and chimps do not share a common ancestor).

Common descent is consistent with theistic evolution, and, of course, with modern evolutionary theory. It is not consistent with the creationist claim that God produced the various "kinds" of organisms separately.

Common descent is a fascinating issue in the evolution debate for a number of reasons as we shall see...

Michael Denton and Common Descent

Michael Denton is an "intelligent design" advocate who wrote a book, Evolution: A Theory in Crisis, published in 1985. In the book he spent a lot of time arguing against common descent. However, he subsequently abandoned his claims. In his later book, Nature's Destiny, he embraces common descent. The fact that the author of these arguments now accepts they are flawed does not concern the creationist one jot. Their faith informs then common descent is wrong, and so they accept any argument against it, without bothering to actually think.

Here is what Denton has actually said (from here):

It is important to emphasize at the outset that the argument presented here is entirely consistent with the basic naturalistic assumption of modern science - that the cosmos is a seamless unity which can be comprehended ultimately in its entirety by human reason and in which all phenomena, including life and evolution and the origin of man, are ultimately explicable in terms of natural processes. This is an assumption which is entirely opposed to that of the so-called "special creationist school". According to special creationism, living organisms are not natural forms, whose origin and design were built into the laws of nature from the beginning, but rather contingent forms analogous in essence to human artifacts, the result of a series of supernatural acts, involving the suspension of natural law. Contrary to the creationist position, the whole argument presented here is critically dependent on the presumption of the unbroken continuity of the organic world - that is, on the reality of organic evolution and on the presumption that all living organisms on earth are natural forms in the profoundest sense of the word, no less natural than salt crystals, atoms, waterfalls, or galaxies. (Nature's Destiny, pages xvii-xviii).

Dave Scot and Common Descent


Dave Scot is an IDist who at one time ran the Uncommon Descent blog site for William Dembski. Here is what he says of objections to common descent (ironic, given the name of the blog):

You certainly don’t have to agree here with descent with modification from a common ancestor but I’m going to start clamping down on anyone positively arguing against it. It’s simply counter-productive to our goals and reinforces the idea that ID is religion because nothing but religion argues against descent with modification from a common ancestor.

This was the thread he said it on:
http://www.uncommondescent.com/index.php/archives/744

Uncommon Descent has a revisionist attitude to history, and Scot's thread has since been deleted (perhaps by Dembski, who rejects common descent, which does explain the name of the web site). The thread is preserved here:
http://immunoblogging.blogspot.com/2006/01/intelligent-design-has-new-party-line.html

Predictions from Common Descent


Common descent is a scientific claim. That means that certain prediction follow inevitably if it is true, and those predictions can be tested. If common descent is true, then certain features of the biological world have to be true. If they are not, then common descent is refuted.

A Nested Hierarchy


Common descent involves a "tree of life" in which, over billions of years, species branch off, evolve and die out. If you can reconstruct that tree, and point to any node in it, it necessarily follows that all the organisms that are descended from the organism at that node are closer related than those not (for example all mammals are descended from a common ancestor, and so are much more alike than those animals that are not). Follow the branch down (i.e., back in time), and pick another node somewhere along it. Now you have a larger set of organisms descended from an older ancestor, which includes the first node, and must necessarily include all the organisms that branched from the first node - just as your grandson's children must necessarily be related to you (so the mammals are all nested inside the vertebrates, because the common ancestor of the mammals was itself a descendant of te common ancestor of all vertebrates). The organisms from the first node are necessarily nested inside the organisms from the second node (your grandson's descendants are nested inside the grouping of your descendants). Thus a nested hierarchy has to be the case if common descent is true.

Curiously, the nested hierarchy was first shown by a creationist, Linnaeus. In fact, it should be noted that the discovery of the nested hierarchy actually predates Darwin's theory of evolution. Predictions in science do not have to be made before the event, they just have to be a necessary consequence of the theory (the orbit of Mercury was well known before Einstein used relativity to predict it, for instance).

A Common Fundamental Chemistry


If all life is descended from a single ancestor, you would expect some of the basic biochemistry of that ancestory to survive in every organism today, at a bare minimum, the mechanism of inheritance. All life on this planet uses DNA/RNA to handle genetic code, and it all codes for amino acids in the same way. The relationship between the three nucleotide codon mapping to a certain amino acid is pretty much universal across all living things.

Codons are discussed here:
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html

Molecular Relatedness Closely Fits Phenotype Relatedness


The prediction is that if two species are similar, and are near each other in the tree of life, then this is because they are closely related, and a necessary consequence of common descent is that their biochemistry is also closely related.




It turns out that proteins can vary quite a lot. The famous one here is cytochrome-c, which is about 100 amino acids long, 30 of which are specific, the other 70 can vary somewhat, without having any impact on functionality. The prediction from common descent, then, is that the variation in cytochrome-c is large for organisms a long way apart in the tree of life, and small for closely related organisms. And this is what we find.

For more, go here:
http://www.rtis.com/nat/user/elsberry/evobio/evc/argresp/sequence.html

In fact, we find this with all proteins. In some cases the protein is only present in one branch of the tree, so can only be tested for in a small group of organisms. Also you can reach a saturation point with some proteins; the variation is too great to get meaningful results for more distantly related organism. Neither of these issues refute common descent; they are what you would expect.

Compare to creation; why would the supposed design bother with different sequences anyway? They all do exactly the same thing. If he craves diversity, why swap the sequences around in such a specific manner?

Friday, 11 January 2013

Intelligent Designer of the Gaps

This is prompted by a post by the Discovery Institute:

Once Again, Why Intelligent Design Is Not a "God-of-the-Gaps"

Centuries ago, man had a poor understanding of nature, and attributed all sorts of natural forces, such as lightning, earthquakes and even the seasons to their gods. Over time, people have come to realise that there are mundane (i.e., not supernatural) reasons for these things, and slowly gods or God is being removed from our understanding of how the universe works. God (in one view) is left as lord of the gaps in our knowledge, and as science progresses, those gaps get ever smaller.

Intelligent Design is "God-of-the-gaps" exactly because it exploits those gaps. Ancient man could not explain lightning, so assumed a supernatural intelligent agency was responsible. Modern man cannot the origin of life (not well enough for certain people anyway), so IDists feel they can assume a supernatural intelligent agency was responsible.

No Positive Evidence


Real science deals with positive evidence; a scientist devises a hypothesis, then offers evidence that supports the hypothesis.

The Discovery Institute's pseudoscience is not like that. They deal with negative evidence; they devise a hypothesis (well, take it from the Bible, and hide the religion), but instead of offering evidence for their hypothesis, they give (supposed) evidence against the competing hypothesis - evolution principally.

If evolution turns out to be wrong, why should we assume that ID must therefore be true? They never say - they cannot because they have no evidence for their claims. In science, if there is no well-supported hypothesis, we say we do not know. In pseudoscience, if there is no well-supported hypothesis, you just assume your own pet theory is true.

ID and God-of-the-gaps


Examples of God-of-the-gaps in ID include:

Dembski's explanatory filter: Basically this say if it was unlikely to have formed by nature, then we should assume Dembski's pet theory is true.

Behe's intrinsic complexity: This claims that if evolution could not produce the IC system, then we should assume Behe's pet theory is true.

With regards to Dembski's claims, the DI article says:

A design inference is not triggered by any phenomenon that we cannot yet explain. Rather, it is triggered when two conditions are met. First, the event must be exceedingly improbable (so much so that it exhausts the available probabilistic resources). Second, it must conform to a meaningful or independently given pattern.

Sure, it is not trigger by any phenomenon that we cannot yet explain; it is triggered by specific phenomenon that we cannot yet explain. That is still God-of-the-gaps. It is still inserting God into something we do not properly understand yet.

Comparing to Real Science


The article says:

Does a forensic scientist commit an "arson-of-the-gaps" fallacy in inferring that a fire was started deliberately rather than by natural causes?

This is an excellent question the author raises. Do forensic scientists infer arson if they cannot explain it by natural causes? I would hope not! I would imagine they look for evidence for arson before they conclude arson. If they cannot find evience for either, the result is that they do not know. This is science, not pseudoscience; you do not get to assume your pet theory when the other hypothesis fails.


I will note that the second part to ID is argument by analogy. That is, if a natural thing has a designed analogue, then the natural thing is probably designed. This is not God-of-the-gaps, but neither is it science.


Monday, 7 January 2013

On Satan

Satan, Lucifer and the snake in the Garden of Eden: All these things have been corrupted by Christian to become something that in the Old Testament they are not. I have discussed the snake elsewhere. Lucifer appears in Isaiah, and if you read the context, is about a dead Babylonian King, and the text makes that very clear.

Isaiah 14:3 On the day the Lord gives you relief from your suffering and turmoil and from the harsh labor forced on you, 4 you will take up this taunt against the king of Babylon:

Satan and Job

This page is about Satan, and will look especially at Satan in Job. Was Satan opposing God when the events in the Book of Job occurred? The usual Christian belief is that he was, but the evidence suggests otherwise...

According to here and here and here in the original Hebrew, whenever satan is mentioned in Job, it actually says "the satan"; this indicates that "satan" was a title or position, rather than a specific individual.

The satan is an angel who has been appointed by God as the adversary, an angel who will test a person's faith by trying to tempt him to the "dark side". Certainly the satan is a tempter, but he is a tempter working for God' divine purpose, not for his own evil reasons.

Let us see what it says in Job...
The satan presents himself to God along with all the other angels:

Job 1:6 One day the angels came to present themselves before the Lord, and Satan also came with them. 7 The Lord said to Satan, “Where have you come from?”
Satan answered the Lord, “From roaming throughout the earth, going back and forth on it.”

This is reasonable, because this was just an angel who has been appointed to be the satan, and part of the role involves touring the world looking for bad people. Christian theology would have us believe that when ultimate evil presents itself to God, God merely asks what he has been doing recently!

Everything the satan does is done with God's blessing, as verse 12 makes clear, because this is an angel that God has appointed to be the satan:

Job 1:12 The Lord said to Satan, “Very well, then, everything he has is in your power, but on the man himself do not lay a finger.”

At the end of Job, God specifically accepts responsibility for all the bad things that happened to Job - because the satan had been acting under God's orders, to test Job:

Job 42: 11 All his brothers and sisters and everyone who had known him before came and ate with him in his house. They comforted and consoled him over all the trouble the Lord had brought on him, and each one gave him a piece of silver[a] and a gold ring.

That makes no sense in the Christian theology - all the bad things happened because of evil Satan. It only makes sense when we realise that the satan was acting under God's remit.

Let us think about the theology a bit more. Christianity, besides the trinity, has Satan who is not as powerful as God, but is certainly comparable to the pagan gods in power, and clearly working to his own agenda. Christianity can explain bad things by blaming Satan.

In a true monotheism, there is no bad god to blame things on, so why does bad stuff happen? The lesson from Job is that it is God testing us, and if you pass the test you will be rewarded. Sure, God and the satan are opposed, but they are opposed because that is what the satan is there to do. It is his job to tempt people to the "dark side", because God wants to see if we will succomb to that temptation.

Remember that bit in the Lord's prayer: "Lead us not into temptation". Why should we pray that God not lead to temptation, unless tempting was part of what God does? In Christian theology you should be asking Satan not to tempt you, because he is the tempter and answers to no one. In Judaism, this request makes sense, because temptation comes from the satan, who is acting under God's authority.

What They Say

A certain JP Holding has a page on the subject of the satan in Job:
http://www.tektonics.org/qt/satansame.html

Holding says "Satan's role is as a tempter, and he claims to own the world (Matthew 4:9 and parallels)." He takes some time supporting the claim that satan is the tempter in Job - and this is consistent with what I said above. It is the satan's appointed task to tempt people to test them for God.

Now let me ask critics a question: In Job, Satan says that he has been "going to and fro in the earth, and from walking up and down in it." Now given his character, what is it that critics suppose Satan to have been doing while he was wandering around the earth? He was undoubtedly looking after his own interests. And since his primary interest in Job is to turn Job away from God, isn't it logical in context that whatever else he was doing was intended to serve the same interest?
Easy enough to answer. What the satan was doing was tempting people on God's behalf to see if they are worthy.

Holding says "He was undoubtedly looking after his own interests" but that is just assuming the conclusion he purports to prove. He does this later too: "Once again, when we realize that Satan in Job was probably engaged in activities to benefit his own agenda, it's obvious that these titles are not promotions but rather recognitions." Sure, if we assume Satan in Job was probably engaged in activities to benefit his own agenda, then its obvious that Satan is evil. But if we abandon that assumption, and instead assume that the satan was an angel working for God, we come to a quite different conclusion. And the latter assumption would seem to fit the original Hebrew.

Satan makes no "request" in Job but issues a challenge of honor, and there is nothing at all, Biblically, against Satan being able to be in God's presence at this point in history, any more than it is a problem that sinful men can be in the presence of the Shekinah.

[The Shekinah, by the way, is the dwelling of the divine presence, especially in the tabernacle and temple in Jerusalem.]

Holding wants us to believe that God had no problem having the most evil being in the universe in his presence. And conversely that the most evil being in the universe has no problem entering God's presence. Perfect good and utter evil, sitting down for a cozy chat. I have to wonder why unutterable evil would want or be able to approach God. I have to wonder why a perfectly good God would allow unutterable evil to be in his presence. And yet, here they are, having a conversation.

He also says "at this point in history", and I am not sure why. Presumably God has not changed, what with him being unchangeable and all. So it suggests Holding thinks Satan has changed between then and (I guess) the NT, and yet the web page seems to be saying it is the same Satan. As I say, not sure about that one.

The other thing I find fascinating is this "challenge of honor". It paints God and the satan as two boys in the school yard, and one says, "I dare you to..." Seriously, this is the divine being, all-power, all-knowing, and Satan goads him into all that befalls Job. I would have guessed the supreme being would be a bit more mature than that. But what do I know?

Of course, the whole "challenge of honor" thing is a fabrication. The Book of Job is about God, and his relationship with man; it s not about the satan at all - he is just part of the scenery. This is about God testing Job's faith, and God uses the satan to set up the test. For most of the book, people are discussing the nature of God, because what the book is about is why God allows (or causes) bad things to happen to good people. In Christian theology, that is because of Satan, but the people in Job do not discuss Satan at all; he is not relevant to the theology here. In Judaism, bad things happen because God is testing you (though his agent the satan), so it makes sense to discuss God's nature when bad things happen to a good man.

Numbers

If you check the Hebrew for Numbers 22:22 (eg here) you will make the surprising discovery that God sent the satan to stand in the road before Balaam. That makes no sense if Satan is a fallen angel, but is perfectly reasonable if the satan is an angel working under God's direction.

It is interesting that no Christian Bible makes this clear. Of course not, they have their own agenda to promote, and that trumps God's holy word every time.

Now this is a blog about creationism first and foremost. The only reason to believe the claims of creationism is that that is what the Bible says. Ironic then that Christianity will ignore what the Bible says if it gets in the way of their theology!