Creationism questions

[Ben]

Originally posted by batgirl:
** When you say that they don’t share homology, how much difference are we talking about, i.e. are there differences in amino acids but the amino acids the same type (e.g. a glutamic acid instead of an aspartic acid) or are they completely different (e.g. a glutamic acid instead of an isoleucine)
**

I mean they are totally and completely different in that if you calculate their sequence homology using a PAM or BLOSUM matrix, it comes out to be chance or less. If you put the proteins through AllAll or MultAlin, no alignment can be produced. (Translation for nonspecialists: “John went to the store” and “Jim went in the store” have high homology, whereas “John went to the store” and “Call me Ishmael” have zero homology.)

batgirl, think of all the serine proteases you can think of- are they all just minor variations on trypsin/chymotrypsin/elastase? Clearly those three are the same protein with differences in binding pocket, so why was the serine protease reinvented so many times? Why have metalloproteases, aspartic proteases, etc. when serine proteases get the job done just fine?

**
You also mentioned homologous proteins with different functions; could you provide an example?**

Take almost any protein and sent it through a BLAST search (for you nonspecialists, it’s a database search that looks up homologous proteins) and you’ll probably find homologous proteins of different function. Vertebrate lens crystallin is famously homologous to a metabolic protein, but I forget which one. A striking example is gelsolin, which has six highly homologous domains of identical fold, but all of which have different functions (one binds to actin, one binds calcium, I believe one severs actin, etc.) Gelsolin combines two problems: the calcium-binding domain is needlessly modelled on the actin-binding domain, when it could have been based on the ultimate calcium-binding protein (like calmodulin.)

**
As for minor differences (rat hemoglobin, chimp hemoglobin, etc.) could at least partially be explained by random mutation since creation. I don’t think anyone disputes that mutation occurrs and in 6000 years one could expect to see a number of non-letal mutations appearing. If one knew the spontaneous mutation rate one could even calculate approximately how many mutations one would expect to see.**

But your system implies that any phylogenetic tree would show all organisms at an identical distance from a common “ancestor” (in this case, God’s perfect archetypal proteins.) In reality, phylogenetic trees based on DNA match those based on the fossil record to a surprising degree of detail- like I said, even the fact that insects came onto land before vertebrates is recorded in their DNA. Similarly, molluscs and vertebrates developed eye lenses separately- and that’s written in their DNA too. If you know how to read it, the DNA is like a history book.

-Ben

[jab1]

First of all, I apologize to batgirl. I no longer think you are Phaedrus. As for being a poor speller, well, Einstein couldn’t do simple arithmetic. It’s a paradox, but extremely brilliant people seem to have difficulty doing simple things.

Originally posted by cmkeller:
Simple answer: G-d created the universe with consistent physical laws because the predictability of science enables better service of G-d. Therefore, when he created the universe, he created it with evidence consistent with “oldness” in order that we can learn science to aid in our future use of those principles. In the same sort of way, G-d created Adam and Eve as adults rather than as newborn babies; he created an adult universe rather than an infant universe.

Great. That means the universe is like an art forgery, like a new bronze statue made to look like an authentic antique from ancient Greece or Rome. You want to believe in a God that deceives you like that, go right ahead.

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>< DARWIN >
__L___L

[Scylla]

Seeing as we have a couple of molecular biologists hanging around, I was wondering if I might interrupt this thread to ask an opinion or two:

Concerning the abiogenesis event and what some consider the problem of complex bacterial forms evolving so quickly in Earth’s early history, do you see Panspermia as a viable possibility?

What existing organisms might be the likeliest candidates for panspermic bacteria?

We know that some bacteria have ssurvived in stasis for 230 million years and returned to viability. DO you see an upward limit in years to bacterial survival in these circumstances?

[Ben]

Originally posted by Scylla:
**
Concerning the abiogenesis event and what some consider the problem of complex bacterial forms evolving so quickly in Earth’s early history, do you see Panspermia as a viable possibility?

**

It’s certainly a testable hypothesis, but I don’t know the specifics. For example, has anyone considered the conditions on Mars at the time life started on Earth?

**
What existing organisms might be the likeliest candidates for panspermic bacteria?

**

That’s like asking what existing organisms might be the likeliest candidates to be Burgess shale organisms. It was billions of years ago- at the very least they would have undergone taxonomic extinction (in other words, evolved into a new species so that the “old” species no longer existed as such.)

I should also point out the tardigrade, which is a multicellular microorganism that lives in moss. It is the toughest organism in existence- if it dries out, it forms a spore in which its cells fill with a sugar that maintains their shape in the absence of water, and thus preserves the integrity of the cellular components. It can survive hard vacuum. Why? The sugar protects the cells. It can survive liquid helium. Why? the sugar protects the cells. It can survive hard radiation. Why? The sugar protects the cells. Tardigrades even travel in the stratosphere, but are they the ancestor of all life? Do tardigrades come from space? Obviously not.

**
We know that some bacteria have ssurvived in stasis for 230 million years and returned to viability. DO you see an upward limit in years to bacterial survival in these circumstances?**

Yes- ultimately radiation damage would chip away at the DNA until it was nonfunctional.

How do we know that they survived so long in stasis?
-Ben

[Spiritus_Mundi]

Lib,
I think I missed the irony.

That, batgirl, is because you lack several months worth of contextual experience with which to judge Libertarian’s bon mots. This particular one can be translated:

[Libertarian] really needs to get some new bumber stickers.

BTW, I am glad you can appreciate light humor but distressed that you continue to use words like “improbable” to describe the likelihood of events for which you have no basis to assign a probability. Remember, if the geologists are correct we are speaking of a time scale in the billions of years. Saying that it is hard to reproduce in a laboratory under controlled conditions is hardly a dmning condemnation.

BTW[sup]2[/sup]: I was aware of teh Cubs Wolrd Series history. My allusion was to an event so “rare” that it could obviously happen only once in teh history of the Earth. Damn, they’re never as funny when I explain them.

---

The best lack all conviction
The worst are full of passionate intensity.
*

[Scylla]

Ben:

We know these bacteria have survived because they have been recovered from Permian salt deposits in Mexico and from the date of the deposit we know they have been effectively freeze-dried for the last 230 million years.

Why are tardigrades not candidates?

[Ben]

Originally posted by Scylla:
**Ben:

We know these bacteria have survived because they have been recovered from Permian salt deposits in Mexico and from the date of the deposit we know they have been effectively freeze-dried for the last 230 million years.

**

Ah, thanks.

**
Why are tardigrades not candidates?**

Lots of reasons:

1. Molecular phylogenies say no.

2. What did they eat during the time that they were the only lifeforms on Earth?

3. They have mitochondria- you would be positing that their mitochondria gained enough functionality to become independent, left their cells, and then evolved into bacteria, some of which became chloroplasts, which then shacked up with plant cells, and then finally the tardigrades would have a food source.

4. Tardigrades, AFAIK, should leave microfossils- if such had been found in the oldest rocks, it would have settled the panspermia question instantly. Remember, these are multicelled animals.

-Ben

[Ben]

Originally posted by batgirl:
I cannot accept abiogenesis because it requires a number of highly unlikely events - it has nothing to do with my being there or not being there.

Nonetheless, you reject the entirety of evolution after that point in favor of a young-earth belief which requires you to throw out much of modern science. If you are truly addressing this question scientifically, then why not accept theistic evolution, if your main scientific problem is with abiogenesis?

Let me also say this: what I’m getting at with my questions about protein homology is, how do you do your work? I’m not trying to disparage your work, but it’s just that it seems to me that you get a new protein to work on, you take its sequence to Pedro’s, and… what? What do you do next? I mean, homology is an important tool in molecular biology, but you don’t seem to have thought about it in any degree of detail, and you don’t even seem to have thought about facts of protein homology that I would have expected you to have dealt with in your work. If I get a new protein, I immediately run it through BLAST and AllAll because I know that the active site of the protein will be the most conserved, that insertions are more likely to be in loops, etc. My evolutionary explanation of homology enables me to tell a lot about the protein. But your explanation? BLAST turns up a lot of identical proteins from other species, because God didn’t need to reinvent the wheel. What does that tell you that could possibly be of use in your work?

In short, why do you work with protein homology at all? What does it tell you? How do you interpret the results?

-Ben

[jab1]

I’m discovering how little I know about proteins. Thanks, Ben.

batgirl, if the universe is only 5760 years old, give or take a decade, why does it LOOK billions of years old?

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>< DARWIN >
__L___L

[Ben]

Originally posted by jab1:
**I’m discovering how little I know about proteins. Thanks, Ben.
**

Let me also say that I know I’m slipping into some molecular biology jargon, so let me know if clarification is needed or if you have any questions.

-Ben

[cmkeller]

jab1:

Great. That means the universe is like an art forgery, like a new bronze statue made to look like an authentic antique from ancient Greece or Rome. You want to believe in a God that deceives you like that, go right ahead.

No, G-d did not deceive us; he told us quite clearly that it was created more recently. He made it look otherwise in order that the science involved in it would be useful to us.

Of course, G-d only told us in the Bible. So if you don’t believe in it, you don’t believe he told us anything. But then again, if you don’t believe in it, you don’t believe in the young Earth anyway.

But either way, there’s no deception here.

Chaim Mattis Keller

[Spiritus_Mundi]

CMKeller,
I think that the reason some of us think that the “created old” postition is deceptive is that there really seems to be no reason for it. There is no reason why the science of a young universe would not be as useful as the science of an old universe. The Young Earth position implies an inherent deception, or at least misdirection, on the part of god, either in the physical laws which He created or in the Biblical account of creation. Those two sources ontradict each other; they cannot both be literally correct. If God is directly responsible for both, then god has deliberately attempted to mislead people.

The best lack all conviction
The worst are full of passionate intensity.
*

[Fillet]

Batgirl,

In my Webster’s dictionary I find the following definitions:

faith: 1. Act or state of wholeheartedly and steadfastly believing in the existence, power and benevolence of a supreme being. 2. Firm or unquestioning belief in something for which there is no proof.

** scientific method**: The principles and procedures used in the systematic pursuit of intersubjectively accessible knowledge and involving as necessary conditions the recognition and formulation of a problem, the collection of data through observation and if possible experiment, the formulation of hypotheses, and the testing and confirmation of the hypotheses formulated.

In light of these definitions, do you see the fundamental disconnect between science and faith, and why they really can’t “reinforce each other” unless you engage in some mental gymnastics? Not that you can’t if you really want to, but you need to acknowledge what you’re doing.

There have been a whole bunch of threads that discuss this topic, many from the creationist vs. evolutionist perspective. Look at these, for example (just skip over the brief gratuitous comments where people engage in mud-slinging):

http:/www.straightdope.com/ubb/Forum7/HTML/000004.html
http:/www.straightdope.com/ubb/Forum7/HTML/000031.html
http:/www.straightdope.com/ubb/Forum7/HTML/000058.html
http:/www.straightdope.com/ubb/Forum7/HTML/000078.html
http:/www.straightdope.com/ubb/Forum7/HTML/000219.html
http:/www.straightdope.com/ubb/Forum7/HTML/000305.html
http:/www.straightdope.com/ubb/Forum7/HTML/000310.html
http:/www.straightdope.com/ubb/Forum7/HTML/0000628.html
http:/www.straightdope.com/ubb/Forum7/HTML/000696.html

I was going to discuss a bit more how mixing science and faith would lead to difficulties in the advancement of your scientific career, but I see Ben is already heading in that direction (thanks, Ben, for re-appearing!). You never did answer my earlier question, either, about what you would do if you found that a hypothesis you were testing turned out not to be viable.

I must admit that I have found it hard to understand how you came to adopt a creationist stance based on science’s inability to readily resolve a fundamental question (i.e., where did life come from?). I could be wrong, but I think that the religious folk on the board would agree with me when I say that this conundrum is a rather poor basis for adopting a particular system of religious belief.

So I’ll make a WAG here: your adoption of creationist beliefs is the by-product of a conversion to more fundamentalist views caused by other things happening in your life, and it has nothing to do with the origins-of-life issue.

One of my friends once said that his graduate student years were the loneliest times of his life, partly because the huge time commitment left him little time for his family, and partly because maybe two people other than himself understood how difficult his dissertation topic really was. I think he hit the nail right on the head. How folks respond to this sort of alienation depends on the circumstances. But I don’t think it’s that uncommon for people who are feeling lost or empty, through either a real or perceived lack of emotional support from friends or family, to seek emotional comfort in the bounds of a group (frequently a religious congregation) that seems to offer what they’re missing.

I’m not going to get into any debates here about whether that’s proper, etc. Frankly, I’m a firm believer (no pun intended) in letting people believe whatever they want as long as they don’t try to impose their worldview on me.

But if that sort of thing is what really happened in your case, it is disingenuous to say that science’s inability to address a particular issue led to your present religious beliefs.

For Scylla: The Permian salt deposits of the southwestern U.S. and Mexico formed via evaporation of shallow seas in a hot arid climate. If any of the organisms fond in the salt domes are indeed remnants of this time (and that has not yet been conclusively demonstrated), then they were desiccated and salted, not freeze-dried.

[Fillet]

Ack! Sorry about all the bolding. Damned codes…

[cmkeller]

Spiritus Mundi:

I think that the reason some of us think that the “created old” postition is deceptive is that there really seems to be no reason for it. There is no reason why the science of a young universe would not be as useful as the science of an old universe.

Interesting hypothesis, but where’s the support? What kind of scientific rules do you think would apply to a “young” universe that actually has living, thinking beings inhabiting it?

No doubt G-d (being omnipotent and all) could have arranged something, but all things considered, physics as we have learned it seems to be pretty darned handy.

If God is directly responsible for both, then god has deliberately attempted to mislead people.

As I said, if you don’t believe in the Bible, you don’t believe in the young Earth anyway, and if you do believe in it, there’s no misleading. If someone creates an imitation Ming Vase and tells you “This doesn’t really date from the Ming Dynasty, and the closest it’s ever been to China is the take-out place down the street,” he’s not deceiving you.

Chaim Mattis Keller

[Cooper]

If someone creates an imitation Ming Vase and tells you “This doesn’t really date from the Ming Dynasty, and the closest it’s ever been to China is the take-out place down the street,” he’s not deceiving you.

In your case, the analogy is: “This doesn’t really date to the Ming Dynasty, in fact, there is no Ming Dynasty, all the records of it are lies, in fact there is no China either, everyone that thinks they are from China spontaeneously appeared in San Francisco with memories of being from a land called China”. THAT is your hypothesis.

Incidentally, no where is it stated in the bible that the universe is a sham designed to produce some sort of ‘scientific enlightenment’ (that is worthless anyway since the only true knowledge can come from the bible).

My goodness! You have to believe such convoluted things in order to get by! I really pity you.

[batgirl]

Wow, lots of posts since I left yesterday afternoon. I don’t have time to comment on all of them now, but I do want to make a few points.

Fillet,

I have revised hypotheses and, in fact, am in the process of doing so right now. The lab I work in is studying signal transduction proteins involved in asthma and a protein we thought was involved may not be, but at this point the data are inconclusive. Part of the problem we’re having is that someone in the group has a lot invested in a particular protein being involved and is determined to demonstrate that it is, so he’s making life difficult for us that think that maybe it’s not.

As for your hypothesis that unhappiness in graduate school led me to my religious beliefs, you couldn’t be more wrong. I both got married and had my son while in graduate school, so despite the long hours and low pay it was a very happy time in my life.

Ben and Fillet,

I don’t work on protein homology.

I can’t find it now, but somebody wrote something along the lines of “other scientists accept your work so why do you question the work of other scientists.” Would that that were true. I have never given a seminar without having my work questioned and I can’t recall ever being at a seminar where the speaker wasn’t given a pretty rough time by someone trying to challenge the methodology or conclusions of the speaker. I like to think that questioning another person’s work is all part of the process at getting at the truth.

I know I didn’t respond to most of the points made, but I wanted to get at least a few for now. Gotta get back to work.

[jab1]

It’s been stated before on this board and I wish I could remember who said it first:

If God could create a universe that looked ancient the day it was made, then He could’ve created it a week ago last Thursday, including our memories of whatever “happened” before that day, including the writing of the Bible itself. The Bible itself could be only ten days old, but with false memories, you’d never know the difference.

For everyone here, I have a link to a page written by Mitchell Plummer and Fred Phillips of New Mexico Tech. It’s Plummer’s Master’s thesis. It shows how a good scientist should be willing to study ANYTHING, because you never know what mundane or disgusting item might be the key to further knowledge of How It Happened: http://griffy.nmt.edu/%7Emplummer/rats/rat%5Fresearch.html

What he studied is the ratio of Chlorine 36 to regular chlorine in the middens of ancient packrats. In other words, he looked at rat droppings. And he did so to see if Cl-36 was produced at the same rate that C-14 is produced. And C-14 and Cl-36 are produced by cosmic rays; the strength of the Earth’s magnetic field determines how many of these rays get through. A weak field means many rays, a strong field means few.

If the ratios of Cl-36 to Cl-37 are comparable to the ratios of C-14 to C-12, we can be more sure that C-14 is a valid way to date ancient materials.

And that’s EXACTLY what Plummer concluded. The production of Cl-36 in the past 12,500 years was comparable with the production of C-14 over the same span of time. See his conclusions at the bottom of the page.

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>< DARWIN >
__L___L

[KeithB]

batgirl wrote:

I can’t find it now, but somebody wrote something along the lines of “other scientists accept your work so why do you question the work of other scientists.” Would that that were true. I have never given a seminar without having my work questioned and I can’t recall ever being at a seminar where the speaker wasn’t given a pretty rough time by someone trying to challenge the methodology or conclusions of the speaker. I like to think that questioning another person’s work is all part of the process at getting at the truth.

<<end quote>>

Ah! But what if you are not familiar with the field? And besides, at some point, as more and more replications are performed, your work and the work of others in the field gets synthesized into a settled consensus and it becomes perverse to question it anymore.

My point is that most of the science that you question is at the consensus stage. In fact, I would say that radioactive dating is past that stage and has become a routine technique for dating rocks. (It is a difficult technique, and requires a lot of care, but it is now more of a technology than a science.)

[cmkeller]

Cooper:

In your case, the analogy is: “This doesn’t really date to the Ming Dynasty, in fact, there is no Ming Dynasty, all the records of it are lies, in fact there is no China either, everyone that thinks they are from China spontaeneously appeared in San Francisco with memories of being from a land called China”. THAT is your hypothesis.

Thanks for telling me what my hypothesis is. I never would have guessed.

Care to explain why you feel a need to exaggerate my analogy?

Incidentally, no where is it stated in the bible that the universe is a sham designed to produce some sort of ‘scientific enlightenment’ (that is worthless anyway since the only true knowledge can come from the bible).

Granted. However, it does say that the universe has been in existence only since 2448 years before it (the Bible) was presented at Sinai (which, according to the Orthodox Jewish record of history, was 3312 years ago). What G-d’s purpose in creating an older-seeming universe might be is modern speculation, and I’ll grant that. However, considering that we’re learning many principles of physics from the way the universe is structured, I’m hazarding a guess that these scientific principles exist for us to put to our own use.

My goodness! You have to believe such convoluted things in order to get by! I really pity you.

Pity is unwarranted. I’m quite happy with my life, thank you.

jab1:

If God could create a universe that looked ancient the day it was made, then He could’ve created it a week ago last Thursday, including our memories of whatever “happened” before that day, including the writing of the Bible itself. The Bible itself could be only ten days old, but with false memories, you’d never know the difference.

You know, you’re 100% right about that. I’d certainly be the last one to claim that G-d can’t do something like that.

However, in life, we have to live according to the evidence of our senses and external data. I don’t have anything at all that says that the universe, despite appearances, was created last week. I do have something that says it was (despite appearances) created 5760 years ago, which I consider credible. Hence, while I’ll concede that it (i.e., the universe) could have happened in a way not described either by the Bible or by science, I have no basis to believe it did.

Chaim Mattis Keller