Monday, May 17, 2010

By Golly!!! It's All True!!!! WE PROVED IT WITHOUT A FLIPPIN DOUBT (see awesome assumptions)

So I meander over to hotair.com today, and see the provocative news article title, Darwin’s theory of universal common ancestry confirmed, which linked to the article, First Large-Scale Formal Quantitative Test Confirms Darwin's Theory of Universal Common Ancestry.


So, apparently all shadows of doubt have been removed from the quest to confirm that we all descend from a single common ancestor of the single-cellular-puddle-of-muck kind! Well this is an awful big assertion, and should be huge news! However, knowing how often the popular science media manipulates their evolution article titles (saying something completely different within the actual article) I did something novel and...read the article. About halfway through, I find what I figured I was going to find. A crapload of circular reasoning. It turns out that "Theobald's study rests on several simple assumptions about how the diversity of modern proteins arose." Woah, wait....? This glaringly vehement pronouncement rests on a few key assumptions!??!? Well let's see what these are.

First, he assumed that genetic copies of a protein can be multiplied during reproduction, such as when one parent gives a copy of one of their genes to several of their children. Second, he assumed that a process of replication and mutation over the eons may modify these proteins from their ancestral versions. These two factors, then, should have created the differences in the modern versions of these proteins we see throughout life today. Lastly, he assumed that genetic changes in one species don't affect mutations in another species -- for example, genetic mutations in kangaroos don't affect those in humans.

So basically, he assumes that it is a process of evolution controlled by the mechanism of natural selection that has led to the vast diversity we see today, and then constructs a test to see how what he is trying to prove happened.........um.........So he assumes universal common ancestry (UCA) through slight mutations and then formulates an experiment to run around those assumptions. He's certainly claiming an awful lot based on some pretty sketchy assumptions.

The article continues:

But do the processes in these assumptions link humans to other animals? Do these processes link animals to other eukaryotes? Do these processes link eukaryotes to the other domains of life, bacteria and archaea? The answer to each of these questions turns out to be a resounding yes.
It does? Really? Could you tell me how we came to the assumptions that the rest of this study (which I'm sure used my tax dollars) is founded upon, and would collapse without? How do we know that "a process of replication and mutation over the eons may modify these proteins from their ancestral version"? Furthermore, the article doesn't tell us how this study shows us that UCA is so plausible a conclusion. It just says that Theobald did some study that proves UCA, believe us you stupid idiots.


I'm sorry, it take a bit more than an emphatic assertion to convince me. The title just shows the blatant dishonesty of the science media when dealing with this issue. It's provocative but presumptuous. How about a study that isn't based on such blatant question begging?

38 comments:

snemes said...

I'm not sure there's a problem there. In science, when you test a hypothesis, you assume that it's true and draw some kind of implications from the hypthosis, which are basically what you'd expect to see if the hypothesis were true. Then, you go and see if that's what you find: if you do, then your hypothesis is supported by the data, and if not, then your hypothesis is not supported by the data.

Their assuming the mechanisms of evolution to check the data is standard scientific practice, and it isn't necessary out of place or improper. Of course, it doesn't prove evolution true without a doubt--no amount of empirical data-gathering could do that, except perhaps if we received word from God that it was so--but then again, so what? It just makes it more probably true (if you adopt a realist view about science).

bossmanham said...

It's one big question beg. I understand how science works, my problem is with the claim that this confirms darwinian evolution without a shadow of a doubt, as the article would want one to believe. It does no such thing. I'm not even sure there's a test that could do that.

heir assuming the mechanisms of evolution to check the data is standard scientific practice,

Which is part of the problem. No one has ever observed this process. It is an extrapolation far beyond the evidence we have. Don't feed the public the bullcrap that "we've proved it--all further scientific inquiry into the issue is no longer needed." That's not true at all. They've at best created a model of how their preconceived history of the world worked, nothing better.

bossmanham said...

I love this comment from joe_dofu on the hotair comment section:

"Falsifiability doesn’t mean you look at the evidence, make a theory about what you’ve already seen, and then challenge people to disprove it based on the same evidence. If it did, then I could make a theory that the sky is blue because it’s full of smurf juice, and then test my hypothesis by checking to see if the sky is blue. Can you prove the sky isn’t blue? No. I didn’t think so."

That's essentially what the scientific community has done w/ neo-Darwinian evolution; not to mention all the ad hoc adjustments to the theory as things like the Cambrian explosion are discovered.

David said...

I understand that you read an article that described Theobald's research, but did you go to Nature to read the Theobald paper itself? If you read the original paper, it might answer some of your questions and objections.

I understand that you object to Theobald's assumptions, but why? What, specifically, is wrong with each of the three assumptions? Why are these assumptions invalid as descriptions of how the natural world works?

David said...

By the way, maybe I missed it, but can you tell me where the article says that "all shadows of doubt have been removed"?

bossmanham said...

What, specifically, is wrong with each of the three assumptions?

I don't see anything wrong with the first assumption, that "genetic copies of a protein can be multiplied during reproduction." That seems to be obvious. But his second assumption, "that a process of replication and mutation over the eons may modify these proteins from their ancestral versions" is exactly what is up for debate here. If he uses this assumption, then he's already assuming what he's setting out to prove. What is his basis for assuming this? It's never been observed, so to claim that this experiment somehow proves UCA is misleading. It only seems to support it if you assume that these mutations, through natural selection, are a sufficient mechanism for producing the diversity of life we see.

By the way, maybe I missed it, but can you tell me where the article says that "all shadows of doubt have been removed"?

The title of the article; "Confirms Darwin's Theory of UCA!!!11!!!". Science media always does this. Missing link here, Java man there...

I don't know that Theobald himself actually made the claim, since I don't have access to his actual article. I'm criticizing this particular characterization of Theobald's work, not Theobald's actual essay (though if he claims this is fool-proof evidence, then he should be called out).

David said...

Is the assumption "that a process of replication and mutation over the eons may modify these proteins from their ancestral versions" invalid?

Nope. We've seen this happen. Most recently, it happened in the strain of the flu virus that was ancestral to the latest H1N1 flu strain. There are many, many other observations of the kind of change assumed by Theobald. Note that the assumption in question does not include the assumption that "these mutations, through natural selection, are a sufficient mechanism for producing the diversity of life". Now, I think that this second assumption has also been repeatedly demonstrated, but that doesn't matter. Theobald is not making this assumption. He's just assuming that "replication and mutation over the eons may modify these proteins from their ancestral versions". And he's right about that.

As far as the title of the article goes, "confirmation" is not the same as "all shadows of doubt have been removed". It's understood in science that confirmation means that a given experiment produced results that are consistent with the predictions of a testable hypothesis. Now, if we keep getting confirmation, then confidence in the hypothesis rises. In some cases, repeated testing has led to great confidence in certain ideas. But everyone in science understands that no theory is ever totally, conclusively proven forever and ever.

If you wish to complain about the way the media covers science, you'll find that many scientists are also unhappy about the way science is covered by the media. But what can you do? Scientists do not control the media.

bossmanham said...

Is the assumption "that a process of replication and mutation over the eons may modify these proteins from their ancestral versions" invalid?

That's what is up for debate. Is there justification for assuming that? I don't think there is.

Most recently, it happened in the strain of the flu virus that was ancestral to the latest H1N1 flu strain

No one is questioning the existence of genetic mutations. What I am questioning is "a process of replication and mutation over the eons may modify these proteins from their ancestral versions." This is fairly ambiguous, but since the article says UCA is confirmed, I presume it is speaking about controversial aspects of whether genetic mutation is sufficient for UCA. You can't assume that it is sufficient for proteins to simply mutate to show that UCA is possible.

If you wish to complain about the way the media covers science, you'll find that many scientists are also unhappy about the way science is covered by the media. But what can you do? Scientists do not control the media.

I wasn't blaming scientists, unless Theobald is claiming the same thing the title of this article claims. If his experiment is consistent with his model, then that is fine. It doesn't prove UCA any more than me pointing to an extant tree proves God created it.

David said...

"What I am questioning is "a process of replication and mutation over the eons may modify these proteins from their ancestral versions."

But mutation DOES modify proteins from their ancestral versions. Just google "mutation new genes".

Here's a non-controversial example. Even within the human population, new alleles (and proteins) for a given gene arise all of the time. Geneticist can use these differences to determine approximately when you shared a common ancestor with someone else in your extended family, or going farther back in time, with someone else in your ethnic group, or going even farther back in time, with any other human on earth.

That's is, as a result of mutation, we differ from each other in our alleles (and in the protein products of these alleles), and we can use these differences to determine degree of relatedness, time of common ancestors and to show common ancestry for all humans. If a process of replication and mutation over the eons did NOT modify these proteins from their ancestral versions, then we couldn't do any of this. The fact that we CAN do this tells you that Theobald's assmumptions are valid.


"This is fairly ambiguous, but since the article says UCA is confirmed, I presume it is speaking about controversial aspects of whether genetic mutation is sufficient for UCA. You can't assume that it is sufficient for proteins to simply mutate to show that UCA is possible."

I'm not sure that I understand. What do you mean by "whether genetic mutation is sufficient for UCA? I don't think that "sufficiency" matters here. We're not talking about whether or not the mutations improve survival, we're just talking about whether mutations modify ancestral proteins and whether or these changes can be inherited. This has been documents thousands of different times.

I think that you may be confusing the question of whether evolution happened (whether or not species share a common ancestry) with the question of the role of natural selection in evolution. The mutation in questions may have no effect on survival whatsoever; this is true for the vast majority of changes used by geneticists to do the human population stuff referred to above. They mutations just have to modify ancestral proteins. That's it. Again, it's not an assumption that this happens, it's a fact.

bossmanham said...

I only have a second at the moment, but I'll interact further later on.

On this: But mutation DOES modify proteins from their ancestral versions. Just google "mutation new genes".

Here's a non-controversial example. Even within the human population, new alleles (and proteins) for a given gene arise all of the time. Geneticist can use these differences to determine approximately when you shared a common ancestor with someone else in your extended family, or going farther back in time, with someone else in your ethnic group, or going even farther back in time, with any other human on earth.


I want to say that that is fine. What one has to assume for UCA is what the next sentence says in the article, "These two factors, then, should have created the differences in the modern versions of these proteins we see throughout life today." That is what may be assumed, but from examining breeding and, as Behe has done with Malaria, we actually see a boundary to nat. sel. that doesn't seem to be able to be surpassed by the natural process. Therefore that assumption is unwarranted, IMO.

I'll tackle the rest later.

David said...

"These two factors, then, should have created the differences in the modern versions of these proteins we see throughout life today."

Yes, if evolution is accurate, then this would have followed, but this is actually more of description of an hypothesis to be tested then it is an "assumption". At the very least, it's a testable assumption.

We agree that mutation can create inheritable differences, yes? Ok, so then the question is...did the diffences generated by these "factors" create a taxonomic distribution pattern consistent with what we'd expect to find if evolution happened? That is, are the data consistent with the predictions made by the common ancestry version of evolution? Before the research is done, Theobald doesn't know if the results will support or contradict evolution.

The key point is that if common ancestry evolution is not an accurate description of the history of life on earth, then there is no reason why we should see the pattern that we see. If life did not evolve, then there could be an infinite number of other possible patterns. Any of the infinite number of possible patterns could have contradicted the theory of comman ancestor evolution. In fact, as the article notes, the data and patterns observed DID contradict certain other views about evolutionary relationships, so clearly, the starting assumptions did NOT dictate the results and conclusions.

Yes, assumptions are made, but the assumptions are either supported by previous observation, or at the very least, we can test their validity. Yes, we make assumptions, but if the assumptions are not valid, then the real world should show us that they are not valid.

David said...

Behe's "boundary" does not exist. and specifically, his conclusion about drug-resistant malaria have been repeatedly debunked.

http://www.sciencemag.org/cgi/content/full/316/5830/1427

http://pandasthumb.org/archives/2007/11/behe-replies-to.html#more

By the way, what can we conclude about the nature of God if drug-resistant malaria is DESIGNED?

And oddly, Behe thinks that humans and chimps share a common ancestor. So, how did humans evolve from a common ancestor with chimps if not by the mechanisms that Behe claims are insufficient? Apparently, there is no boundary that prevents humans from evolving from apes.

David said...

Oops. Looks like there's a problem with a link address.

Try the following...all on one line.

http://www.sciencemag.org/cgi/
content/full/316/5830/1427

bossmanham said...

Yes, if evolution is accurate, then this would have followed

It's being assumed in an experiment which they claim proves UCA. My point exactly. Question begging. This is so often the case with this silly, and what has become ad hoc, hypothesis. No empirical evidence, just a bunch of assumptions.

We agree that mutation can create inheritable differences, yes?

Yeah, that's been observed. How far those mutations go is another story.

Yes, assumptions are made, but the assumptions are either supported by previous observation, or at the very least, we can test their validity.

He's assuming that what he is testing is possible. He's assuming that this actually happens with no empirical evidence. Then he runs a test to see how it happens the way he's already envisioned it.

They're taking Darwin's hypothesis, formed from observing some natural selection, and extrapolating far beyond that evidence to say that common descent through nat sel is the case. Then Theobald formulates a method to show exactly how that happened. So they're assuming it happened and then showing how it would happen. You're never going to prove yourself wrong that way.

Yes, we make assumptions, but if the assumptions are not valid, then the real world should show us that they are not valid.

Not necessarily. Not if you are already assuming something beyond the empirical evidence and continue to modify the existing hypothesis to match the evidence, as Rho has been showing you in the other thread.

Behe's "boundary" does not exist. and specifically, his conclusion about drug-resistant malaria have been repeatedly debunked.

Uhm, I tend to disbelieve atheists with a stick up their rear about Behe. You all are so vitriolic against the man; it's silly. These little websites meant to debunk him are nothing to me. I may consider actual scientific reviews that question his conclusions, and will consider Carroll (though he's got an ax to grind himself), but often the claim that he's been "DEBUNKED" is far exaggerated. And from your continued lack of understanding of the way logic works, I'm not going to take your word for it.

By the way, what can we conclude about the nature of God if drug-resistant malaria is DESIGNED?

I don't mind thinking that something God created as good mutated due to the effects of sin to cause harm to people. Or it could have introduced it into the world as a result of sin. Or it could have been something that existed from the beginning and because of human degeneration, we are now susceptible to it.
---
BTW, the point from Behe's writing on malaria I am referring to was about how it couldn't adapt to sickle cell anemia.

And Behe has responded to Carroll as well. It's a bit dishonest to act as if there's only one side to the story.

And oddly, Behe thinks that humans and chimps share a common ancestor.

I'm aware of that. It doesn't matter here.

David said...

“He's assuming that what he is testing is possible. He's assuming that this actually happens with no empirical evidence. Then he runs a test to see how it happens the way he's already envisioned it. They're taking Darwin's hypothesis, formed from observing some natural selection, and extrapolating far beyond that evidence to say that common descent through nat sel is the case. Then Theobald formulates a method to show exactly how that happened. So they're assuming it happened and then showing how it would happen. You're never going to prove yourself wrong that way.”

You’re really missing the point here. If Theobald runs a test to “see how it happens the way he’s already envisioned it”…and if he is WRONG…then his test will show that he’s wrong! If the extrapolation is wrong, then his test will show that the extrapolation is wrong! Theobald is NOT formulating a method to test natural selection. He’s NOT formulating a method to show how evolution happened. He’s deliberating attempting to DISPROVE the hypothesis of common descent, and if common descent is wrong, then the data should show it.

Theobald does NOT know before the research is done if he’ll get the sort of pattern that I described to you with respect to human populations. If there is no common descent, then any number of different patterns might be observed. As it happens, the pattern observed supports the hypothesis. Sorry about that.
By the way, are you ever going to read the actual Theobald paper? How can you say anything at all about this research if you haven’t read the original paper?

David said...

“These little websites meant to debunk Behe are nothing to me.”

Well, they should be if they’re based on good science. Unfortunately, Behe has a habit of not keeping up with the literature. See the Dover Trial.


“I may consider actual scientific reviews that question his conclusions, and will consider Carroll (though he's got an ax to grind himself), but often the claim that he's been "DEBUNKED" is far exaggerated.”

I can change my word if you’d like, but the point is that observations in the real world have already shown that much of what Behe claims can’t happen actually does happen. For example, Behe will say that if two mutations are required to do something, then it can’t happen. But there are examples where this has happened. This is what I mean by “debunked”.


“I don't mind thinking that something God created as good mutated due to the effects of sin to cause harm to people.”

But the point is that Behe claimed that mutations producing drug resistance could NOT occur, regardless of whether or not mutation is due to the “effects of sin”. Behe says that something created as good by God can NOT become harmful and/or drug-resistant by mutation. So, God MUST have create malaria as BAD.


“Or it could have been something that existed from the beginning and because of human degeneration, we are now susceptible to it.”

Not likely. Use of quinine-type drugs is a very recent invention. Drug-resistance has nothing to do with the relative susceptibility of the host.


“BTW, the point from Behe's writing on malaria I am referring to was about how it couldn't adapt to sickle cell anemia.”

Ah, well, since Behe has made a very big deal about the number of mutations required for drug resistance, I thought that this is what you were referring to. In any event, I don’t know of anyone who would claim that organisms can always get the mutations that they need to survive. Sometimes they get what they need, and sometimes they don’t. That’s why we have extinction.


>And oddly, Behe thinks that humans and chimps share a common ancestor.

"I'm aware of that. It doesn't matter here."

Why not? Behe claims that there are all kinds of boundaries that prevent even relatively minor changes such as the ones discussed under “malaria”. The series of mutations and other events required to produce chimps and humans from a common ancestor are much, much greater and much more extensive than the changes in malaria already discussed. So, if Behe thinks that evolution can produce chimps and humans from a common ancestor, then he’s clearly admitting that the kinds of boundaries he claims exists do not, in fact, really exist. You can’t claim that mutation can’t account for certain traits in malaria while simultaneously acknowledging common ancestry for chimps and humans. If chimps and humans share a common ancestor, the Behe is clearly wrong when he talks about “boundaries” with respect to evolution in malaria.
In other words, Behe debunks Behe.

bossmanham said...

If Theobald runs a test to “see how it happens the way he’s already envisioned it”…and if he is WRONG…then his test will show that he’s wrong!

Not if the test ASSUMES that it happened. If the test is not dealing with the empirical data of what they say happened, UCA, and is simply dealing with their preconceived notions, there is no way that test is going to disprove what they are assuming in order to run the test! The test is built upon that assumption, as the article states.

They aren't questioning that assumption in the test and trying to falsify it, they are assuming it is true and then running this Bayesian algorithm including their assumption. You can do this with anything and get the results you want. If you assume something is true, the test won't necessarily reveal it to be wrong.

For example, Behe will say that if two mutations are required to do something, then it can’t happen. But there are examples where this has happened. This is what I mean by “debunked”.

Which just confirms that you don't know what you're talking about. Behe says, in the post I linked to, "But I certainly do not say that multiple amino acid replacements “can’t happen”. A centerpiece of The Edge of Evolution is that it can and did happen. I stress in Chapter 3 that in the case of malarial resistance to chloroquine, multiple necessary mutations did happen in the membrane protein PfCRT. I also of course emphasize that it took a huge population size, one that would not be available to larger organisms. But Carroll seems uninterested in making distinctions."

You silly internet atheists don't actually read the sources you are criticizing and don't understand the arguments. You rely on second and third hand sources and then peddle their lies around. This is why I don't take your word for anything.

If chimps and humans share a common ancestor, the Behe is clearly wrong when he talks about “boundaries” with respect to evolution in malaria.
In other words, Behe debunks Behe.


Or David shows that David has never read nor cared to understand Behe.

The papers Carroll cites to "debunk" Behe only say that "different species have different protein binding sites (but, although the authors assume Darwinian processes, they demonstrate nothing about how the sites arose); or B) different species have different protein networks (but, again, the authors demonstrate nothing about how the networks arose). Like Jerry Coyne, Sean Carroll simply begs the question. Like Coyne, Carroll assumes whatever exists in biology arose by Darwinian processes. Apparently Darwinism has eroded Coyne’s and Carroll’s ability to separate data from theory."

Behe says, "In fact, the data I cite in The Edge of Evolution is a real demonstration. While we have studied them, in a truly astronomical number of chances, a variety of microbes developed precisely none of the sophisticated cellular mechanisms that Darwinist imaginations ascribe to random mutation and selection. That data demonstrates random mutation doesn’t explain the elegance of cellular systems."

Behe comes to the same conclusion I do, that you're begging the question.

bossmanham said...

It's clear you don't understand how scientific tests work. Yes you must assume things when testing other things. But when you're assuming one thing to demonstrate another, you ARE NOT guaranteed success, because what you assume may not be touched in the current test. If I assume Dawinian evolution and then test microbial genetic stuctures, I could come away with the conclusion that they are related. But that's not necessarily the case. I am assuming that Darwinian evolution was the mechanism that caused the different microbes to exist only if I assume Darwinism. But what if we don't assume it? We can't make the same conclusion.

But I suppose this is what happens when you put your blind faith in evolutionary biologists.

I would suggest you stop with your dishonesty about Behe, because it's disingenuous and intellectually dishonest. You've never read his works, and I doubt you've read his detractor's works. You googled what I was talking about and found the quickest blurb you could to "refute" what I was saying. I've seen it too much to be taken in by your silliness.

David said...

Theobald.

"Not if the test ASSUMES that it happened.”

The test does NOT assume that it happened. The test is designed to detect the patterns that we’d expect IF it happened. If it DIDN'T happen, then the pattern will be different and the test will fail to confirm the hypothesis that it happened.

I’m not sure that I’ve made myself clear. Let me try again.

Let’s say that common ancestry is wrong. God created separate kinds (whatever a kind is), the kinds do not share common ancestors. Let’s say that this is the way the world really is and that this is the actual history of life on Earth.

Now, let’s consider the differences among these kinds in 23 universally conserved proteins. If kinds do NOT share a common ancestor, what sort of pattern of differences would you expect to find? Any reason to expect any consistent pattern at all?

Let’s study these patterns using the same type of tools that we use to study differences in human alleles. When we use these tools, they detect a pattern of allelic changes that shows that humans dispersed around the world from a common ancestral population, that is, they show that all humans have a common ancestor. When these methods are used to show that all humans have a common ancestor, I assume that you have no objection to the methods.

Ok, we apply the tools to the data from 23 universally conserved proteins. If the reality is that common ancestry is wrong, why would these tools conclude that there is a pattern consistent with the hypothesis of common ancestry? Why wouldn't the actual pattern in the data be much more random? There is simply no reason to think that these tools would find any such pattern if the pattern didn’t exist. The research would probably indicate that apes and oranges are equally likely to be our closest relatives.

Why, specifically, exactly would the research produce a conclusion of common ancestry when the data are generated by organisms that lack a common ancestor? Saying “they made assumptions” is not enough. Explain how, exactly, the computer program works and how, exactly, it draws its conclusions and why, exactly, it would produce the wrong answer from the protein data.

David said...

Behe.

You’re right, I’ve read little by Behe since I read “Darwin’s Black Box” many, many years ago, but I’ve watched the man for fifteen years, and you don’t have to read everything he’s written to see his game. Basically, Behe looks around the edges of what is known and what is unknown, and when he finds something that is not thoroughly explained, he says “God did it”.

Now, this is a fool-proof strategy, because there’s always something that is not well understood, so Behe can play this game until he dies. It’s as unbeatable as the declaration that “God is good”, because the only way to prove Behe wrong is to know absolutely everything about absolutely everything. Not going to happen, so Behe wins.

I once heard Behe speak (that’s right, I sat through an entire Behe talk and even asked a question at the end), and he was asked how ID and its variants could be disproved, and he said that ID would be disproved when science had explained everything. Really, that’s what he said. Obviously, that’s not a valid disproof, but it works for Behe. The real question is…if Behe is wrong, how can we know that he’s wrong without having to do the impossible like explain absolutely everything first?

Behe is really good at one thing, and that’s moving the goalposts. First he’ll say that science can’t explain A, so God did it. Then someone explains A, so Behe says, but science can’t explain B, so God did it. Then someone explains B, so Behe moves the goal posts and says science can’t explain C, so God did it.

This has been going on since Darwin’s Black Box, in which Behe said…

“By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution.”

Note the phrase “ANY ONE OF THE PARTS”.

Well, almost as soon as the book was published, scientists began showing Behe complex systems in which one part was indeed removed, and the system worked just fine anyway. That should have ended it, but Behe just went off to look for something else that hadn’t been explained.

David said...

You’re right about one thing. I was confused about the two mutations in malaria issue. Behe does indeed say that it’s possible to get new traits this way, but only just barely, as he calculates the odds of this happening at on in 10 to the power of 20. However, he’s being a bit disingenuous when he says “but I certainly do not say that multiple amino acid replacements can’t happen”, because he does say that the odds against a three mutation change are so great as to make it essentially impossible (to me, “multiple” suggests at least three changes and not just two.). He’ll go for two, but not for three.

Of course, if you’ve read the criticisms of Behe, then you should be aware of the fact that there are very good reasons to think that Behe’s one in 10 to the power of 20 number is totally bogus due to the invalid assumptions that went into the calculations. Garbage in, garbage out.

So, two mutation traits can evolve in malaria. However, this does mean that a two mutation trait can only evolve in huge population of microorganism, and so as Behe says…

"On average, for humans to achieve a mutation like this by chance, we would need to wait a 100 million times 10 million years. Since that is many times the age of the universe, it's reasonable to conclude the following: No mutation that is of the same complexity as chloroquine resistance in malaria arose by Darwinian evolution in the line leading to humans in the past 10 million years".

If that's a fact, and Behe says it is, then it’s impossible that chimps and humans could be the product of evolutionary events that included a common ancestor at about 7 million years ago. And yet, Behe accepts the common ancestry of chimps and humans. So how do we get humans from an ape-like ancestor when “no mutation that is of the same complexity as chloroquine resistance in malaria arose by Darwinian evolution in the line leading to humans in the past 10 million years”? Again, Behe debunks Behe.

What’s the mechanism that produced humans from apes. God did it? And how did God do it? How does God cause mutation? Anyone ever observed God causing mutation? No one has ever seen “sophisticated cellular mechanisms” arise from nothingness, let alone, seen God create a single need hominid species. And why go through all those hominid intermediates first? Couldn’t God get it right the first time? It’s all well and good to say that we haven’t evolution produce such and such, but I’ve never seen God do it either.
Now, you can argue that these are theological issues, but really, that’s the point. ID and its variants are really just theology. That would be ok with me, but I wish they’d just admit it and be honest about it.

(It’s remarkable how much you complain in these last comments about folks making “assumptions”. Seems odd for the master of assumptions.)

bossmanham said...

The test does NOT assume that it happened

"First, he assumed that genetic copies of a protein can be multiplied during reproduction, such as when one parent gives a copy of one of their genes to several of their children. Second, he assumed that a process of replication and mutation over the eons may modify these proteins from their ancestral versions. These two factors, then, should have created the differences in the modern versions of these proteins we see throughout life today"

It is what he's assuming. He's not trying to falsify that, he's constructing a test to see "whether the evolutionary relationships among living organisms are best described by a single 'family tree' or rather by multiple" and in that assumes that the way life propagated itself was through the processes of mutation.

But what if we don't assume this? These patterns in the alleles could be as such for a number of reasons. Perhaps there are patterns in the genetic structures because all species live in similar environments (ie the earth's environment). Perhaps a designer found that certain genetic traits were efficient to use in many different species. If we don't assume that pattern = relation and that must be the only way to construe the evidence, there may be many different conclusions one could reach. If we ever observe random mutations through nat sel as sufficient to diversify a species in the way neo-Darwinism claims, then we can assume what Theobald assumes. Otherwise, that assumption is unfounded.

Basically, Behe looks around the edges of what is known and what is unknown, and when he finds something that is not thoroughly explained, he says “God did it”.

Another reason to disregard you completely, David. You atheists constantly do this with the ID movement. You simply apply the "godidit" tag to them when their reasoning is far more subtle than that. Why not actually deal with their arguments instead of straw men?

Behe is really good at one thing, and that’s moving the goalposts

I've thought the same about most evolutionary biologists.

Well, almost as soon as the book was published, scientists began showing Behe complex systems in which one part was indeed removed, and the system worked just fine anyway.

I notice we have here an unbacked assertion. Show such an example, and in doing so, don't misrepresent what Behe means by "irreducibly complex." Ken Miller, if you are referring to him, tried to show that removing certain parts of the flagellum motor leaves us with the type III secretory system. Well yeah, but that doesn't mean the flagellum isn't irreducibly complex, it means that there is a subsystem of the motor that can function as something else. But notice we lose cell motility in the loss of the motor. This line of argument is like arguing that the drive train of a car isn't irreducibly complex because the lights still work even if the engine or wheels are removed.

Behe isn't the only one who has notice the limited potential in nat sel, as Barry Hall's experiments with E. Coli showed a similar limitation when he removed their lactase enzyme, as seen here.

It’s remarkable how much you complain in these last comments about folks making “assumptions”. Seems odd for the master of assumptions

Another misrepresentation. Should we call you the master of that? First off, I'm not complaining about assumptions, I'm complaining about claiming you've proven something based on unfounded assumptions.

Second, how do you figure I'm the "master of assumptions"? All I'm voicing is skepticism in the loudly proclaimed "truth" of neo-Darwinian evolution. I don't make the assumption that mutations and nat sel are sufficient to produce a substantive evolutionary change. Get your facts straight.

David said...

>“These two factors, then, should have created the differences in the modern versions of these proteins we see throughout life today".

“It is what he's assuming.“

No, this is what he’s testing. The factors should have done certain things. Now we test to see if the two factors did what we think they should have done. If they didn’t, the test will show it.

“He's not trying to falsify that, he's constructing a test to see "whether the evolutionary relationships among living organisms are best described by a single 'family tree' “.

And if the evolutionary relationships are not best described by a single family tree, the test will falsify the hypothesis. The potential for falsification was demonstrated by the fact that test did NOT support other views of the history of life on Earth.

“But what if we don't assume this?
These patterns in the alleles could be as such for a number of reasons. Perhaps there are patterns in the genetic structures because all species live in similar environments (ie the earth's environment). Perhaps a designer found that certain genetic traits were efficient to use in many different species.”

Well, yes, God could have set things up so that our test results would deceive us into thinking life evolved. But that’s not Theobald’s fault. He can only uncover the patterns that exist. If you wish to believe that God is a deceiver, that’s your choice. Either way, by saying that there could be other reasons why we see a particular pattern, you are acknowledging that the test is able to distinguish among many different patterns, including patterns that support evolution and patterns that do not.

What if God didn’t decide to put the same alleles in species that appear to be closely related? What if God put the same allele for one of these proteins in both oranges and apes, but not in humans? Then with another protein, the same allele went into yeast and humans, but not apes? Why wouldn’t Theobald’s test pick up on this and generate a conclusion that common ancestry is false? Be specific. Why would the computer program fail to show that there is a big problem with the common descent theory?

“If we ever observe random mutations through nat sel as sufficient to diversify a species in the way neo-Darwinism claims, then we can assume what Theobald assumes. Otherwise, that assumption is unfounded.”

Define “diversify”. What would you accept as an example of “diversity”? Just want to know where the goal posts are.

David said...

“You atheists constantly do this with the ID movement. You simply apply the "godidit" tag to them when their reasoning is far more subtle than that. Why not actually deal with their arguments instead of straw men?”

Ok, so what’s the subtle reasoning? Are you saying that God didn’t do it? Little green men did it? If it’s not evolution, what’s the answer?

“I notice we have here an unbacked assertion. Show such an example, and in doing so, don't misrepresent what Behe means by "irreducibly complex."

Have you read Miller’s books? I think that there are more examples there. But off the top of my head, I’d point to blood clotting proteins. I can’t remember the exact number for humans, but let’s say it’s ten. Now Behe says that you need all (ten) or so for the complex system of blood clotting to work. Take away ANY ONE OF THE PARTS, and the system fails. However, there are other mammal species with few than (ten) clotting proteins. Their blood clots just fine.

“Ken Miller, if you are referring to him, tried to show that removing certain parts of the flagellum motor leaves us with the type III secretory system. Well yeah, but that doesn't mean the flagellum isn't irreducibly complex, it means that there is a subsystem of the motor that can function as something else.”

But that’s all we need in evolution. As long as one part can do something useful, that part can evolve for that reason. It doesn’t have to move the cell in any way. Then, once that part exists, additional changes can add or change functions. What to guess what a flagellum is made of? Secreted proteins.

“But notice we lose cell motility in the loss of the motor. This line of argument is like arguing that the drive train of a car isn't irreducibly complex because the lights still work even if the engine or wheels are removed.”

You’re doing this backwards. You’re looking at the final function, and you’re saying that if we lose a part from the final system, then the whole thing is worthless. You have to start with the light alone which has value by itself as a light. The light can “evolve” for reasons other than propelling the car. Then later, you can add the drive train, adding the function of movement.

This is one of Behe’s big mistakes. He looks at a system as it exists today and ignores its history. He says that if you remove a part today and you break the machine as it exists today, then you can’t build it up from simpler systems. He doesn’t consider the fact that the simpler systems may have worked just fine in the past when the entire system was the simpler system. By Behe’s argument, multi-stone arches can not exist.

bossmanham said...

No, this is what he’s testing.

No, it's contained in the assumptions. He's testing "whether the evolutionary relationships among living organisms are best described by a single 'family tree'". Get your facts straight.

And if the evolutionary relationships are not best described by a single family tree, the test will falsify the hypothesis.

No, it will only falsify the hypothesis that is based on the further assumption, which is unfounded.

Well, yes, God could have set things up so that our test results would deceive us into thinking life evolved.

Why would you think GOd did it to deceive us? Perhaps we just don't view it correctly. Some road signs may be confusing to some people, but that doesn't mean the designers are purposely trying to deceive people. It means that the readers of the signs are mistaken. Nice try, though.

Why would the computer program fail to show that there is a big problem with the common descent theory?

My goal isn't to critique his program. I have no idea what it even looks like. Your search for specific critiques are misguided. I am critiquing a science media article. Keep that straight.

Define “diversify”. What would you accept as an example of “diversity”? Just want to know where the goal posts are.

How about a single cell being the ancestor of all life we now see. That work?

Ok, so what’s the subtle reasoning? Are you saying that God didn’t do it? Little green men did it? If it’s not evolution, what’s the answer?

I think God did something, though I'm not clear on the specifics, but that is due to other beliefs I hold. However, God is not a necessary aspect of ID. ID happens in computer labs all over the world every day, as Rho points out here.

Have you read Miller’s books?

No, my knowledge of this particular controversy is purely web based. I do know that Behe and Miller have responded to each other quite a bit.

I’d point to blood clotting proteins

Then you may want to spruce up on the intricacies of the debate before you go throwing around these straw men you've just posted.

But that’s all we need in evolution. As long as one part can do something useful, that part can evolve for that reason.

Why would a component that has nothing to do with motility and functions just spiffily evolve (quite a bit I might add) to give the cell motility? And wouldn't the cell then lose the function of the secretion device? As Behe says, "The activity of a protein export system has no obvious connection to the activity of a rotary motor propulsion system. Thus the difficulty of accounting for the propulsive function of the flagellum and its irreducible complexity remains unaddressed."

By Behe’s argument, multi-stone arches can not exist.

I wonder if there's some inherent feature in those who blindly follow neo-Darwinian evolution to misrepresent the arguments of those who would dare question its orthodoxy?

David said...

"My goal isn't to critique his program. I have no idea what it even looks like. Your search for specific critiques are misguided. I am critiquing a science media article. Keep that straight."

Ah, finally, some clarity. You’re not critiquing Theobald's program. You don’t actually know how Theobald did the research. You’re just critiquing a science article. So, after all the criticism of how Theobald did his research, you’re not actually criticizing the research, you’re just criticizing the article describing the research.


>Define “diversify”. What would you accept as an example of “diversity”? Just want to know where the goal posts are.

“How about a single cell being the ancestor of all life we now see. That work?”

Could we narrow this down a bit? No other example of diversity produced by mutation will do? Any chance we could start with something a little more modest and smaller scale? There is a character limit to these postings after all.


“I think God did something, though I'm not clear on the specifics.”

Ok, so you think that God did it. So does Behe, and for the same reason as you. So, why get upset when when ID is characterized as “God did it”. I wold add that the “lack of specifics” (read: no mechanism offered at all) is why ID “theory” is considered almost completely useless by science.

“However, God is not a necessary aspect of ID. ID happens in computer labs all over the world every day, as Rho points out here.”

Pointing to computer labs is all well and good, but does anyone out there really believe that the Designer is anything other than God? Anyone think the designer is anything like geeks in a comp lab? Anyone? One can imagine that little green men did it, but no really believes it, and there is zero evidence for this. None. No one has ever seen the LGM, despite the fact that speciation is an ongoing process. Honestly, if a “designer” intervened on Earth, it is far, far easier for me to believe that we’re talking about entity that we call “God” than it is for me to believe it’s space aliens. Please. Can’t anyone in the ID movement just be honest about this.

David said...

>Have you read Miller’s books?

“No.”

Then maybe you should hesitate before pounding me for not reading everything that Behe wrote.


“You may want to spruce up on the intricacies of the (blood clot) debate before you go throwing around these straw men you've just posted.”

Ok, so, Behe says that factors “before the fork” are not essential due to redundancy. But what if an organism lost one of the two branches before the fork? Now the before-the-fork proteins that were once redundant are absolutely essential. If you looked at this organism after these changes occurred, you would conclude that the parts of the cascade before the fork composed an IR system, and so, could not have evolved. But you’d be wrong, because originally, these proteins were NOT a part of an IR system. They only appear to be IR because you don’t realize that they were once part of a redundant system. The problem is one of history. If you don’t know the history of the system, you can’t tell if you’re looking at an IR system or not.

I’ve read some Behe, so you can read some Miller.

http://www.millerandlevine.com/km/evol/DI/clot/Clotting.html

Now, to look at another alleged IR system that isn’t really IR, let’s look at the complement system.
http://www.talkorigins.org/faqs/behe/icsic.html


“Why would a component that has nothing to do with motility and functions just spiffily evolve (quite a bit I might add) to give the cell motility?”

Why not? If a secretory system can also produce motility, that’s obviously going to be something that natural selection will drool over. I’m not sure I follow what’s being said here. But to take guess at what you are saying, if a secreted protein remained attached, and if it moved due to the proton motive force that is already associated with secretory systems, then you’re on your way to a evolution of motility from a component that has nothing to do with motility.

“And wouldn't the cell then lose the function of the secretion device?”

Not necessarily. Yersinia enterocolitica has both a Type III secretory system and is motile by flagella.

http://www.ncbi.nlm.nih.gov/pubmed/10931293
.

“As Behe says, "The activity of a protein export system has no obvious connection to the activity of a rotary motor propulsion system.”

Well, I believe that they both use a proton motive force mechanism to drive their various activities and as I said, the flagellum itself is built by exporting (secreting proteins). So, there we have at least two connections. Others have noted the extraordinary degree of homology between proteins found in the secretory systems and the proteins found the flagellar systems. These homologies also extend to include other proteins in the cell that are not directly involved in either secretion or motility, but which exist for other reasons.


“Thus the difficulty of accounting for the propulsive function of the flagellum and its irreducible complexity remains unaddressed."

Well, yes, if you ignore the data.


>By Behe’s argument, multi-stone arches can not exist.

“I wonder if there's some inherent feature in those who blindly follow neo-Darwinian evolution to misrepresent the arguments of those who would dare question its orthodoxy?”

Ok, care to explain how I misrepresented Behe’s argument?

By the way, any comments on Behe debunking Behe with respect to common ancestry for chimps and humans?

bossmanham said...

David, stop posting these silly links. The issue is the article. You continually want to delve into these red herrings. Enough with it.

bossmanham said...

So, after all the criticism of how Theobald did his research, you’re not actually criticizing the research, you’re just criticizing the article describing the research.

Wow, David. You act like you've solved the mystery of the grassy knoll. I've never claimed to be critiquing Theobald's research itself. As I said earlier, "I don't know that Theobald himself actually made the claim, since I don't have access to his actual article. I'm criticizing this particular characterization of Theobald's work, not Theobald's actual essay." Did you forget I said that, or are you purposely being dishonest to somehow make me look bad?

My criticism is that this article claims this PROVES universal common ancestry. But for that to be true, you have to assume that natural selection and random mutations are a sufficient mechanism for that. The article admits that is one of the assumptions. So, what the experiment may show to be more plausible is, if we assume that natural selection and random mutations are a sufficient mechanism for evolutionary development, then UCA would be the way it happened.

Could we narrow this down a bit? No other example of diversity produced by mutation will do? Any chance we could start with something a little more modest and smaller scale? There is a character limit to these postings after all.

Nope. This is as good as you're going to get.

Ok, so you think that God did it. So does Behe, and for the same reason as you. So, why get upset when when ID is characterized as “God did it”

Because that's not where it stops. The reason you dishonest atheists spout the silly contention is because you want to try to show that ID would shut off scientific inquiry. But you reveal your ignorance of the history of scientific inquiry when you do so. Don't act like it's an innocent label. You know good and well what you're doing.

does anyone out there really believe that the Designer is anything other than God

Dawkins thinks it was aliens.

I think the God hypothesis is the best for many different reasons.

Then maybe you should hesitate before pounding me for not reading everything that Behe wrote.

No, because I'm actually taking time to look into it. I've read Miller's silliness online and I'm not lying about what he says. You are lying about what Behe's position is, as you are claiming he believes one thing when he has clearly stated otherwise.

If a secretory system can also produce motility, that’s obviously going to be something that natural selection will drool over.

You're anthropomorphizing a completely unintelligent, unthinking process. Why would this work in nat sel. As the successive changes happen, the cells gain more and more proteins, but eventually the secretory system will cease to work as such. But we still don't have a completed flagellum. So not only do these intermediate cells lack their spiffily working secretory system, but they can't move either. Where's the improvement?

By the way, any comments on Behe debunking Behe with respect to common ancestry for chimps and humans?

I tend to ignore silly red herrings. Sorry. Behe would probably say there was need of intelligent guidance in the mutation. If you'd actually had any shred of intellectual honesty, you wouldn't even bring up such a silly question.

Any comment on your chronic dishonesty?

David said...

"I've never claimed to be critiquing Theobald's research itself."

Bossman said:

He's assuming that what he is testing is possible. He's assuming that this actually happens with no empirical evidence. Then he runs a test to see how it happens the way he's already envisioned it.

They're taking Darwin's hypothesis, formed from observing some natural selection, and extrapolating far beyond that evidence to say that common descent through nat sel is the case. Then Theobald formulates a method to show exactly how that happened. So they're assuming it happened and then showing how it would happen. You're never going to prove yourself wrong that way.

Not if the test ASSUMES that it happened. If the test is not dealing with the empirical data of what they say happened, UCA, and is simply dealing with their preconceived notions, there is no way that test is going to disprove what they are assuming in order to run the test! The test is built upon that assumption, as the article states.

They aren't questioning that assumption in the test and trying to falsify it, they are assuming it is true and then running this Bayesian algorithm including their assumption. You can do this with anything and get the results you want. If you assume something is true, the test won't necessarily reveal it to be wrong.

End Bossman said.

Wow, if this is how you don't critique research, I'd hate to see what happens when you actually do critique research.

bossmanham said...

And you wonder why I don't trust the modern science media when it breeds people who lie as incessantly as you are.

David said...

The issue is the article. You continually want to delve into these red herrings. Enough with it."

I believe that YOU were the one who introduced Behe into the conversation. I've just been responding to what YOU started.

bossmanham said...

Wow, if this is how you don't critique research, I'd hate to see what happens when you actually do critique research.

I also said, " if he claims this is fool-proof evidence, then he should be called out."

In those quotes, I am assuming what the article states is true. Then I say IF this is what is going on, this is my problem with it.

It's called assuming something is true for the sake of argument. You're still lying.

bossmanham said...

I believe that YOU were the one who introduced Behe into the conversation. I've just been responding to what YOU started.

I mentioned Behe in passing. You began linking to everything but his mother.

David said...

“Because that's not where it stops.”

Well, where else does it go? Again, no one really thinks that the designer is anything other than God. The dishonesty here is on the part of the ID promoters.

“Dawkins thinks it was aliens.”

Now who’s lying? You know very Dawkins doesn’t think it’s aliens.

“I think the God hypothesis is the best for many different reasons.”

Right. The designer is God. What else could the designer be?


“You are lying about what Behe's position is, as you are claiming he believes one thing when he has clearly stated otherwise.”

Not true. I made have made mistakes about what he said, but I have not deliberately lied about it.


“You're anthropomorphizing a completely unintelligent, unthinking process. Why would this work in nat sel.”

Sorry about the antho; it was meant in a joking manner. Why would it work? Because any movement is better than no movement.

“As the successive changes happen, the cells gain more and more proteins, but eventually the secretory system will cease to work as such.”

Why? I don’t understand.

“But we still don't have a completed flagellum. So not only do these intermediate cells lack their spiffily working secretory system, but they can't move either. Where's the improvement?”

Did you miss the point about Yersinia? Cells can have both separate systems. Check out “gene duplication”.


“I tend to ignore silly red herrings. Sorry. Behe would probably say there was need of intelligent guidance in the mutation. If you'd actually had any shred of intellectual honesty, you wouldn't even bring up such a silly question.”

Oh for crying out loud. How is this question dishonest in any way? One Behe statement seems to contradict another. So, is there an explanation? That’s all I’m asking. Why does this bother you so much? Turns out there is an explanation. God did it. Great. Behe saves Behe with an untestable hypothesis.


"Any comment on your chronic dishonesty?"

What dishonesty? I do make the occasional mistake with Behe, in part, because the man is all over the map in his postions (see earlier link to Panda’s Thumb). I’m not deliberately lying about anything.

David said...

"I am assuming what the article states is true."

And you didn't bother to read the Theobald paper to see if it was true?

So, what happened to my link disproving Behe's position that blood clotting is irreducibly complex?

bossmanham said...

"I am assuming what the article states is true."

And you didn't bother to read the Theobald paper to see if it was true?

So, what happened to my link disproving Behe's position that blood clotting is irreducibly complex?


David, in the statement I am assuming it's true. It's shorthand for, "IF WHAT THE ARTICLE SAYS IS TRUE, THEN THEOBALD IS...." Grow up dude, really.

And the link didn't disprove anything. I told you I was sick of all the red herrings you were running off on. The whole thing didn't even address Behe's argument.

Now who’s lying? You know very Dawkins doesn’t think it’s aliens.

Then you didn't watch Expelled.

Because any movement is better than no movement

What's your evidence for that. That isn't necessarily true at all. It's what YOU MUST ASSUME. I don't assume that. If a cell is working perfectly fine, why would it take on cumbersome changes that would limit its function until the evolution process had formed a new component. It's not like a cell all of a sudden pooped out the flagellum out of the secretion system. It was a gradual process that took a long time !!!!!(NOTE, DAVID. I AM ASSUMING SOMETHING TO BE TRUE FOR THE SAKE OF ARGUMENT)!!!!!!

Did you miss the point about Yersinia? Cells can have both separate systems. Check out “gene duplication”.

They have two systems. They don't have one system that changed into another. That is pretty important, since it was you that claims the flagellum descended from the type 3 secretory system.

I would say Yersinina just shows an example of irreducible complexity at work. It has two fully functioning systems, both which would be useless if a part were removed.

Why? I don’t understand.

Well, David, because the flagellum doesn't just get pooped out all of a sudden. It would be a process of proteins being passed on and then built upon in successive generations of the cell. You'd have an in between flagellum/TTSS which would be conceivably quite cumbersome. But since we've never observed this evolution take place, it's all speculation from us both.

I do make the occasional mistake with Behe, in part, because the man is all over the map in his postions

No, it's because you assume he believes something because you have an agenda fueled by the popular press and dishonest scientific popularizers, like Dawkins and Miller, who lie about his positions. Then you go spout it off to me as if it's the gospel truth. You've just run into someone who's pretty skeptical of evolutionary biology.

One Behe statement seems to contradict another.

So you say, but I've shown you to be wrong on multiple occasions. You're still at it with your dishonesty. I'm getting pretty sick of it. I have shown more patience than I've cared to with your slanderous statements about Behe, and he's not really even the issue.

Enough has been said on this post.

bossmanham said...

Really, this telling behavior by your less than honest sources is hampering scientific inquiry. You have guys, like Behe and Meyers, who see that there is something not quite right with the scientific dogma of the day. So they want to question it and test it. But the vatican of science, run by these oh so righteous defenders of truth; Dawkins, Miller, etc, will stop the evil heretics and their disgusting though crimes of even suggesting the neo-Darwinian paradigm is founded on faulty assumptions and incomplete data.

As someone who seems to have an interest in Science, you ought to be appalled by that behavior David. But I think you just don't want the dogma challenged.

Comments are closed here. Email me if you want to continue this discussion.