Common DNA Sequences: Evidence of Evolution or Efficient Design? (apoptosis section fascinating!)

Acts & Facts ^ | August 2009 | Jeffrey Tomkins, Ph.D.

[GodGunsGuts]

With the advent of modern biotechnology, researchers have been able to determine the actual sequence of the roughly three billion bases of DNA (A,T,C,G) that make up the human genome. They have sequenced the genomes of many other types of creatures as well. Scientists have tried to use this new DNA data to find similarities in the DNA sequences of creatures that are supposedly related through evolutionary descent, but do genetic similarities provide evidence for evolution?...

[tacticalogic]

If anyone is obscuring other possibilites that would be the evo-cultists incapable of tolerating any dissent of their cult.

Your opinion is noted, and given all the consideration it's due, based on the evidence presented.

[count-your-change]

Whats’ the point? The point is that you ask others to something you are not willing to do. And then you say there's no point, blah,blah,blah,

Here are the articles (the relevant parts) you call “outdated” but, of course, you offer nothing to support your statement:

“Structure of Chicken Hypothalamic Luteinizing Hormone-releasing
Hormone
II. ISOLATION AND CHARACTERIZATION*
(Received for publication, February 17, 1982)
Judy A. King and Robert P. Millar
From the Department of Chemical Pathology, University of Cape Town Medical School and Groote Schuur Hospital,
Observatory 7925, Cape Town, Republic of South Africa

The decapeptide LH-RH’ (pGlu-His-Trp-Ser-Tyr-Gly-Leu-
Arg-Pro-Gly-NH 2 ), originally isolated from porcine hypothalami
(Matsuo et al., 1971a) and later synthesized (Matsuo
et al., 1971b), appears to have lower gonadotropin-releasing
activity in submammalian vertebrates than in mammals.
Crude hypothalamic extracts from birds, reptiles, amphibians,
and fish, however, contain significant gonadotropin-releasing
activity, and LH-RH-like immunoreactivity has been demonstrated
in the hypothalamus of these vertebrates by radioimmunoassay
and immunocytochemistry (for reviews, see
Ball, 1981; Jackson, 1981; King and Millar, 1981). We have
shown that immunoreactive amphibian hypothalamic LH-RH
is identical with the mammalian decapeptide in chromatographic
properties and in its interaction with region-specific
LH-RH antisera, while immunoreactive LH-RHs from avian,
reptilian, and piscine hypothalami are structurally different
(King and Millar, 1979, 1980, 1981). These structural differences
of LH-RH-like peptides in submammalian vertebrates
have not been determined”

and:

“PMID: 6986260 [PubMed - indexed for MEDLINE]

King JA, Millar RP.
Immunoreactive LHRH was detected in hypothalamic and extrahypothalamic brain extracts of the rat, bird (pigeon and chicken), reptile (tortoise and lizard), amphibian (frog and toad), teleost (cichid), and elasmobranch (dogfish) and in the whole brain of the cyclostome (bagfish). The concentration of hypothalamic immunoreactive LHRH was more than 5-fold greater than that of the extrahypothalamic brain. Mammalian and amphibian hypothalamic immunoreactive LHRH yielded displacement curves parallel to those of synthetic LHRH in assays employing four antisera which recognize different regions of the decapeptide, thus suggesting a similarity in the structure of their LHRH. Hypothalamic immunoreactive LHRH from the bird, reptile, teleost, and elasmobranch differed from the mammalian and amphibian peptide in yielding displacement curves nonparallel to those of synthetic LHRH with three different antisera (1076, 743, and 744) which bind between Trp3 and Pro9 of LHRH. The differenece in structure appears to be near Leu7. With antiserum 422 which binds the NH2- and CO2H- termini of LHRH, bird, reptile, and teleost hypothalamic extracts yielded displacement curves parallel to that of synthetic LHRH. Bird, reptile, and teleost hypothalamic extracts showed displacement curves parallel to each other in all assays. In studies on the relative quantitation of LHRH, all four antisera gave similar values of immunoreactive LHRH concentration in mammalian hypothalamic extracts and in amphibian hypothalamic extracts. By contrast, assay of bird, reptile, teleost, and elasmobranch hypothalamic extracts with antiserum 422 gave much higher values than did the other antisera, suggesting that the LHRH peptide is structurally different from mammalian and amphibian LHRH in the region of Leu7 but similar at the NH2- and CO2H-termini. These conclusions are supported by studies on the biological activity of hypothalamic LHRH from the different species using dispersed ovine anterior pituitary cells in culture. The LH release responses to equivalent amounts of immunoreactive LHRH (as measured by antiserum 422 which binds a region of LHRH essential for biological activity) from the various species were similar, indicating that the biologically active region of the molecule has been conserved in evolution. Structural differences in vertebrate hypothalamic immunoreactive LHRH were confirmed by cation exchange and high pressure liquid chromatography. Our findings of differences and similarities in vertebrate LHRH support a contemporary phylogenetic scheme.”

The very things you complain about are the very things you do, that no one will engage you on a certain subject, that others have preformed opinions, that someone is not being “frank”, or would not be since you can't be bothered to actually ask the source.

So it's off you go to The Braying Chorus. Is that “frank” enough for you?

[Stultis]

Here are the articles (the relevant parts) you call “outdated” but, of course, you offer nothing to support your statement:

Except for everything I did offer. Like the fact that there are multiple LHRHs, BUT THEY DIDN'T KNOW THAT THEN, and that they don't even call them LHRHs in current literature and nomenclature.

Why do I always have to repeat everything three times with you? (And why am I so damn patient about it, even while being griped at and insulted? Just good natured, I guess.)

Oh, and that the first article you're giving me (and for which you don't provide a full cite for some reason)...

“Structure of Chicken Hypothalamic Luteinizing Hormone-releasing Hormone
II. ISOLATION AND CHARACTERIZATION*
(Received for publication, February 17, 1982)
Judy A. King and Robert P. Millar

... is not referenced anywhere in the "Sean D. Pitman M.D." article which CottShop linked. It's the same authors as "Comparative Aspects of Luteinizing Hormone-Releasing Hormone Structure and Function in Vertebrate Phylogeny," but published two years later.

Still, even it makes the point fabulously about being outdated:

The decapeptide LH-RH’ (pGlu-His-Trp-Ser-Tyr-Gly-Leu- Arg-Pro-Gly-NH 2 ), originally isolated from porcine hypothalami (Matsuo et al., 1971a) and later synthesized (Matsuo et al., 1971b), appears to have lower gonadotropin-releasing activity in submammalian vertebrates than in mammals.

Did you notice this CONTRADICTS the finding in their 1980 paper, wherein they inferred (by indirect immunological assay) that human and amphibian LHRH are more similar? Now they find the isolated and synthesized pig LHRH (the only pure isolate they seem to have) is LESS active in submammals.

Crude hypothalamic extracts from birds, reptiles, amphibians, and fish, however, contain significant gonadotropin-releasing activity, and LH-RH-like immunoreactivity has been demonstrated in the hypothalamus of these vertebrates

They still haven't even isolated LHRH in these other ("submammalian") species, let alone done any sequencing, but are only using "crude hypothalamic extracts"!

Sorry, but can you read?

has been demonstrated in the hypothalamus of these vertebrates by radioimmunoassay and immunocytochemistry (for reviews, see Ball, 1981; Jackson, 1981; King and Millar, 1981).

Radioimmunoassay?

Immunocytochemistry?

Crude hypothalamic extracts?

Hello, Hello, HELLO?!

OUTDATED!!!

King JA, Millar RP. Immunoreactive LHRH was detected in hypothalamic and extrahypothalamic brain extracts of the rat, bird (pigeon and chicken), reptile (tortoise and lizard), amphibian (frog and toad), teleost (cichid), and elasmobranch (dogfish) and in the whole brain of the cyclostome (bagfish). The concentration of hypothalamic immunoreactive LHRH was more than 5-fold greater than that of the extrahypothalamic brain. Mammalian and amphibian hypothalamic immunoreactive LHRH yielded displacement curves parallel to those of synthetic LHRH in assays employing four antisera

Yeah, and there's the one that is referenced by Pitman, and which I've already read.

So what was your point? I am wrong in claiming this research is outdated? Well, again, can you read?

Sorry, I really don't understand on what basis you are contesting this. I don't see it at all. The (slightly) newer article you introduce just strengthens the point, since even just two years later the obsolete point Pitman dishonestly extracted had been undermined!

[ofwaihhbtn]

Well, since nucleotides form a natural polymer (they inherently link to one another) they are far, far, far more likely than scrabble pieces, which only assort randomly, don't polymerize, and don't have the complex properties that a polymer has, to form meaningful arrangements.
--Stultis

... there was nothing about either the backbone of the molecule or the way any of the four bases attached to it that made any sequence more likely to form than another. Later I found out that the noted origin-of-life biochemist Bernd-Olaf Kuppers had concluded much the same thing. As he explained,

"The properties of nucleic acids indicate that all the combinatorially possible nucleotide patterns of DNA are, from a chemical point of view, equivalent."

In sum, two features of DNA ensure that "self-organizing" bonding affinities cannot explain the specific arrangement of nucleotide bases in the molecule:

1. there are no bonds between bases along the information-bearing axis of the molecule and
2. there are no differential affinities between the backbone and the specific bases that could account for variations in sequence.

--Stephen C Meyer, Signature in the Cell

Just like the scrabble pieces being dumped out onto the parking lot, the nucleotide bases would, if the process was left entirely to mindless chance, not be arranged in any meaningful way.

[Stultis]

O.K., this is beyond me, but does anyone here know how to query the genome database thingies for sequence similarity information, so we can settle this thing once and for all?

Here's the original claim I responded to again:

There are many other interesting little problems concerning commonly used phylogenic tracing genes and proteins. For example, mammalian and amphibian "luteinizing hormone – releasing hormone" (LHRH) is identical. However, birds, reptiles, and certain fish have a different type of LHRH. Are humans therefore more closely related to frogs than to birds? Not according to standard evolutionary phylogeny trees. Again, the data does not match the classical theory in this particular situation.15" [LINK]

So we need sequence similarity for -- I believe the underlying genes involved are GNRH1 and GNRH2? I think those are the one expressed in the brain -- humans, pigs, some amphibian, and maybe some other submammalian vertebrate, like a reptile or bird. I don't know how to get that data. If someone does it would be nice to put this to rest definitively.

[Stultis]

Just like the scrabble pieces being dumped out onto the parking lot, the nucleotide bases would, if the process was left entirely to mindless chance, not be arranged in any meaningful way.

But they would be arranged in various specific ways. Then, so long as the polymers can reproduce, the relative ease and fidelity with which differing sequence can and do reproduce represents meaningful information.

Scrabble tiles can't and don't encode structural information the way a biopolymer does. We can READ the scrabble tiles, and determine if they are words or gibberish, but they are structurally the same -- just wooden tiles -- either way.

The scrabble tiles only have primary structure (the simple sequence of subunits) and all the information is soley in that sequence, only in the primary structure.

All biopolymers also have secondary structure (local hydrogen bonding) and tertiary structure (3-D molecular shape). Even randomly generated primary structures will have different secondary and tertiary structures, and inevitably some secondary and tertiary structures (and thereby some primary structures) will reproduce better than others. Thus there is meaning ("how well do I reproduce myself?") even to random primary structures (random sequences) provided only that they do reproduce.

Scrabble tiles just don't work like that.

[count-your-change]

It took all of thirty seconds to find this example of use of “luteinizing hormone” in the current literature and nomenclature:

“P2X receptors are expressed on neurons containing luteinizing hormone-releasing hormone in the mouse hypothalamus
linkinghub.elsevier.com/retrieve/pii/S0304394009004790”.
(THIS WENT ONLINE APRIL 2009!) Hello? That would be LHRH.

And I have before me “Goodman and Gilman’s The Pharmacological Basis of Therapeutics, ninth edition 1996”

On page 1363, Chapter 55, it begins a discussion of LUTEINIZING HORMONE and among other others, “(GnRH or LHRH)”
Can you read?
You couldn't find Tomkin's credentials and publications, you can't find the latest nomenclature used.....And you ask if I can read!!!!

Insulted? Like this? “....Pitman dishonestly extracted...”

Your arguments are like a reclaimed landfill, looks good until the surface is scratched and then a load of garbage is discovered, I don't think I want to dig through it to find a few bits of valuable material.

[ofwaihhbtn]

... so long as the polymers can reproduce ...
--Stultis

Reproduction is only possible with much highly specified biological information being in place. We are discussing the origin of that information, so we can't use processes dependent upon its existence to explain its origin.

[Stultis]

Reproduction is only possible with much highly specified biological information being in place.

Yes.

I conceded that already, and affirmed that DNA cannot be the first replicator, nor the first conduit of genetic information.

We are discussing the origin of that information, so we can't use processes dependent upon its existence to explain its origin.

You were. I wasn't. To repeat myself again, the origin of information is no problem. The origin of faithful and persistent replicators is the problem. Once you have such replicators, you will automatically, unavoidably have information.

[Stultis]

Insulted? Like this? “....Pitman dishonestly extracted...”

Your arguments are like a reclaimed landfill, looks good until the surface is scratched and then a load of garbage is discovered

It's not insulting if it's factually accurate. The load of garbage REMAINS that Pitman -- whether strictly dishonestly, or as I also considered, through incompetence -- DID cite outdated, superseded information, because it said what he wanted it to say.

Heck, YOU YOURSELF, count-your-change, introduced an additional paper by the same researchers which UNDERMINED, only two years later, their earlier claim, seized upon twenty four years later by Pitman to claim that this hormone is more similar in humans (actually pigs, since that was the synthesized isolate the researchers had available to them) and amphibians.

Oh, wait, except that Pitman did lie outright also, saying they were "identical," when the researchers only said "similar," and the method they used couldn't possibly have determined they were identical.

In any case, we now know that there is MORE THAN ONE of the GnRH hormones produced in these tissues, and we don't have any way of knowing which were being compared in these comparatively primitive studies. So they mean nothing.

Nothing against Judy A. King and Robert P. Millar, btw. They were working at a time when these hormones were poorly understood. And just because they apparently didn't have the time, inclination or equipment to fully isolate and sequence these substances, doesn't mean it was necessarily wrong to use the synthetic pig hormone to do a bit of probing using various indirect means. But Pitman's misuse of this outdated research, and CottShop's citation thereof, remains a load of crap. Absolutely.

Nice try at avoiding the issue, but no dice.

[ofwaihhbtn]

... the origin of information is no problem.
--Stultis

The origin of information is the problem.

The origin of faithful and persistent replicators is the problem.
--Stultis

"faithful and persistent" replication requires complex, highly specified information.

Once you have such replicators, you will automatically, unavoidably have information.
--Stultis

You have it backwards. Once you have the information required, "faithful and persistent" replication is possible.

[Stultis]

"faithful and persistent" replication requires complex, highly specified information.

We'll just have to disagree on that. A replicator could, potentially, have a basically random primary sequence. Replication is mainly chemistry. Yeah, there will be some structural constraints -- and structure does mean information, even in a primitive replicator -- but nothing remotely like a modern genetic code.

So, yes, some minimal level of information needs to be present initially, just what must be inherent in a structure that can replicate. But it is, I suspect, far from demonstrable that this minimal level is beyond that which can arise in undirected natural systems.

We probably have some rough idea by now what that minimal level is, since as I understand researchers have been creating artificial replicators. (No, doesn't tell us what actually happened, but does model the minimum information and complexity necessary in principle to such entities.) But I've only heard vaguely about this research and am not familiar with the particular findings.

[count-your-change]

You say outdated but still fail to cite anything to contradict what they found. So someone citing their studies, (which the later doe not “undermine” the earlier) is quite proper.

Had you read the first citation you see the researchers used the word “identical” and why they said so. But you know better than they.

“In any case, we now know that there is MORE THAN ONE of the GnRH hormones produced in these tissues, and we don't have any way of knowing which were being compared in these comparatively primitive studies. So they mean nothing.”

GnRH 1 and 2 are discussed in “Endocrinology” here:

endo.endojournals.org/cgi/content/abstract/142/2/830 -

With the salient comment that GnRH 2 was 70% identical to GnRH 1, being an ISOFORM. (that means that are two forms of the same protein and probably irrelevant to function).

This does nothing to negate the earlier studies, nothing.

[ofwaihhbtn]

Thanks for an interesting discussion. I would be curious to know your thoughts on Chapter 14, "RNA World" of Stephen C. Meyer's Signature in the Cell. He makes the case there that the "probabilistic resources" available just aren't sufficient for RNA molecule self replication being arrived at by chance:

Even if an RNA sequence could acquire the replicase function by chance, it could perform that function only if another RNA molecule -- one with a highly specific sequence relative to the original -- arose close by. Thus, in addition to the specificity required to give the first RNA molecule self replicating capability, a second RNA molecule with an extremely specific sequence -- one with essentially the same specificity as the original -- would also have to arise. RNA-world theorists do not explain the origin of the requisite specificity in either the original molecule or its complement. Orgel and Joyce have calculated that to have a reasonable chance of finding two such complementary RNA molecules of a length sufficient to perform catalytic functions would require an RNA library of some 10⁴⁸ RNA molecules. The mass of such a library vastly exceeds the mass of the earth, suggesting the extreme implausibility of the chance origin of a primitive replicator system.

Thanks again.

[Stultis]

Oh.

Wow.

You're really sticking with this line of argument?

Really?!

Earlier I made a joke about rank and file creationists refusing to hold creation scientists accountable. But your performance here, count-your-change, proves it was no joke.

So, O.K. If you insist...

Let's look, in careful detail, at just one tactic you employ to dismiss Pitman's dishonesty (or incompetence, as the case may be):

Had you read the first citation you see the researchers used the word “identical” and why they said so. But you know better than they.

Again (for, what? the third time now? the fourth?) Pitman wrote:

For example, mammalian and amphibian "luteinizing hormone – releasing hormone" (LHRH) is identical.

Note this is a full sentence. He writes that the hormone -- not some partial aspect of the hormone, not data from some immunological probe indirectly detecting the hormone -- but just the hormone "is identical".

However the paper he cites says NO SUCH THING. It says only that they are "similar". That similarity was detected NOT by sequencing the peptide (not even by fully isolating it!) but by probing it with a few antigens (made from a synthesized pig hormone) that could only indirectly detect (bind to) four sites on the hormone.

This is a primitive method by current standards. By its very nature, this test CANNOT POSSIBLY confirm that two molecules are "identical".

Probably you do, but just in case you don't understand antigen reactions, this test only consists of the antigen "saying," in effect: "Hey, I found a particular spot, on some molecule in this solution you put me in, that I can stick myself to. I only know a part of me fits a part of this molecule well enough to stick to it. I have no idea what the whole molecule looks like."

Heck, we don't even know, not for sure, what molecules the antigens were binding to, since the GnRH (LHRH, whatever) hormones were never even isolated. There are, btw, other complexities as well. Unfortunately I'm not expert enough on the subject of neuronal hormones, or biology generally, to sort them out. But, for instance, I'm given to understand that the hormone is not created from the underlying gene directly. Instead a precursor is created. Also, if I understand correctly, and as you would expect of just about any hormone, it's not produced constantly. Indeed its production has to be shut off at certain times and elevated at others (pulsed) just in order for it to do what it does (primarily regulate reproductive functions). Also, although I haven't found a reference on this, I would imagine that levels of the type 1 and type 2 vary on different cycles. (Else why two types produced?)

In any case, there would seem to be many reasons that various affinities might be detected at various times when all you're doing is basically mashing up the hypothalamus and putting the "crude hypothalamic extracts" into a test tube, and injecting some antigens, or doing other INDIRECT tests along similar lines, never really isolating the target hormone. We have no way of knowing, for instance, if the production of GnRH was turned "on" in some of the samples and "off" in others, or if one type was being produced in some hypothalamic tissues at the time the "crude extracts" were taken, and another type in others.

This very dated research JUST ISN'T ANYWHERE REMOTELY NEAR GOOD ENOUGH to be making ANY claims in 2004 (when Pitman wrote his article) about the genomic affinities of mammals and amphibians with respect to this hormone.

But I digress from the specific issue, which is you actively helping Pitman lie about the "identical" bit. So back to that.

Here's where you pretty much give away the game, when you introduce an additional article (the 1982 paper, Structure of Chicken [LHRH]) by the same authors as the 1980 paper Pitman cites.

Up to this point you might have been excused on grounds of missing the point. But by introducing this article -- which is NOT cited by Pitman, nor referenced anywhere in his article, nor anywhere in CottShop's post, nor anywhere else in this thread -- you indicate that you DO get the point: That Pitman DID lie (or incompetently err) about the hormone being "identical" in mammals and amphibians.

So you bring up this additional article out of the blue (which you smugly pretend I dismissed) because it contains the magic word, "identical". But does even this article say the hormone is identical in mammals and amphibians? Not quite:

We have shown that immunoreactive amphibian hypothalamic LH-RH is identical with the mammalian decapeptide in chromatographic properties and in its interaction with region-specific LH-RH antisera, while immunoreactive LH-RHs from avian, reptilian, and piscine hypothalami are structurally different (King and Millar, 1979, 1980, 1981). These structural differences of LH-RH-like peptides in submammalian vertebrates have not been determined

So it turns out this is only referring back to the research done in connection with the 1980 paper. They are not saying the hormone is identical, full stop. They are saying it is identical in certain properties. Certain antisera bind with it, as previously discussed. And "chromatographic properties" (high pressure liquid chromatography, we find from the earlier paper) match, which only means there are similar compounds and concentrations thereof, close enough that identical patterns are produced on the plates. Neither of these findings entail that the hormone is sequence identical.

So, all that trouble and nothing to show. In fact you had to engage in a small deception, misdirection (or error?) yourself, by slipping in the additional article and coyly pretending it had been there all along.

Wouldn't it have been easier to just admit Pitman blew it?

Or is it just always, "creationist MUST be right, evolutionist MUST be wrong" with you?

[count-your-change]

“Probably you do, but just in case you don't understand antigen reactions, this test only consists of the antigen “saying,” in effect: “Hey, I found a particular spot, on some molecule in this solution you put me in, that I can stick myself to. I only know a part of me fits a part of this molecule well enough to stick to it. I have no idea what the whole molecule looks like.”

Antigens are quite specific to antibody sites and the tests are accurate despite your comments.

Calling someone dishonest or incompetent is not holding them accountable and so far you've struck out with no one’s help at all. And you clearly do not understand the tests that were used and which you so easily dismiss.

As for Mr. Pittman, he may say whatever, he is not my concern here. It isn't that those who bend their knee to Darwinism and its doctrines MUST be wrong, they just are.

[Ha Ha Thats Very Logical]

I appreciate your spending so much time on this—it’s very illuminating. As a layman myself, I sometimes read these things and only have a nagging sense that something’s not right but don’t have the time or expertise to figure out exactly what. Like here: I had a suspicion that “behaved the same way in a certain test” was not the same as “are identical.” I could drop a basketball and a tennis ball and record that they both bounced to the same height—that doesn’t make them the same.

[ElectricStrawberry]

In reality, there is a clear demarcation between each created kind (humans, chimps, mice, chickens, dogs, etc.), and there is no blending together or observed transition from one kind of animal to another.

I don't think this Doctor knows that the premise is that animals alive today are claimed to be descendents of common ancestor animals that are no longer around to get a DNA sample from. ....that the premise is that the similarities in the DNA are argued to point to common ancestry from extinct common ancestors. ...that todays animals co-evolved from common ancestors.

What a doofus.

When comparing DNA sequences between animal taxa, evolutionary scientists often hand-select the genes that are commonly shared and more similar (conserved), while giving less attention to categories of DNA sequence that are dissimilar.

Uh.....yeah, Doctor.....THAT'S THE FREAKIN' POINT!!! .....to find and look at the similarities. There would be no freakin' point in looking at the differences when trying to find commonality.

What a doofus.

What is really going on with these types of similar genes and how can they be interpreted within a special creation model as opposed to a naturalistic framework?

So, Doctor, you want to do EXACTLY that which you bemoan evolutionists for doing...looking at the data with an obvious bias towards your desired model.......except your result will always be a false conclusion, Doctor.

What a doofus.

False conclusion, Doctor......what a doofus.

[ElectricStrawberry]

So you think the laws of physics and chemistry plus natural selection explain how the body precisely snips out the tissue between an unborn child’s fingures via apoptosis? Oh, do go on!

I'd dig out my Developmental Biology text........but you wouldn't understand anything I said.

[ElectricStrawberry]

Speaking of Jihad, most people don’t realize that the greatest number of suicide bombers come from a revolutionary branch of the Temple of Darwin

So all them moooooslems are all really atheists? Perfect disguise.

Is there ANYTHING you don't connect to a belief in evolution? Nazis...check. Commies....check. Islamofascists.....check. Muslim suicide bombers......check.

Lunacy.....check.