Obsolete Critiques
by MikeGeneIt is truly a joy to watch the "evolution debates" through the prism of The Design Matrix. For example, Peter Forbes reviews two new books on evolution, including The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution, by Sean B Carroll. Let's conider this review in the light of the DM.

























February 4th, 2008 at 12:55 pm
As Carroll says: "the rule of DNA code is use it or lose it."
I find this an interesting quote, an interesting prediction of neo-Darwinian evolution. However, I have seen some suprisingly strong evidence that there are exceptions to this rule.
Recently there was a report of an experiment with mice where a specific gene was knocked out resulting in, well, supermice. These supermice were more intelligent, stronger, and had more stamina than their undamaged siblings. It would seem that their capacity is limited by a governor gene. In light of "the rule of DNA code is use it or lose it" how is this explained?
Daniel Tammet was apparently born normal. After a head injury he became a savant, currently the most noteable one. Another fellow I saw on TV recently had an incredible memory for detail. In general, you ask him about any day in his life, and he can recite details down to what clothes he wore, and conversations that took place. It would seem that likely these incredible capacity exists in all of us, but that it is not accessible for some reason. If we have vast unused capacity, how does this conform to the rule "use it or lose it"?
Comment by bFast — February 4, 2008 @ 12:55 pm
February 4th, 2008 at 2:51 pm
bfast:
Do you have a reference for this?
Comment by Bradford — February 4, 2008 @ 2:51 pm
February 4th, 2008 at 3:21 pm
I recall hearing about an experiement like this, where the mice where also more likely to get cancer than the normal mice, if I recall correctly.
According to Wikipedia and his personal website, Daniel Tammet has epilepsy, synaesthesia, and Asperger Syndrome. The latter two seem to be inhertited conditions, each with their drawbacks as well as occasional gifts, and not the result of brain injury.
Comment by One Brow — February 4, 2008 @ 3:21 pm
February 4th, 2008 at 3:31 pm
bFast asks:
Hi bFast,
Carroll's point is that DNA that is unexpressed (or expressed but selectively irrelevant) will tend to become corrupted, because mutations in those regions are not as dangerous as mutations in critical parts of the genome.
Unused capacity doesn't necessarily imply unexpressed DNA. Lot of interesting things can happen when you simply change the relative rates of expression of genes. Also, environmental forces (like Tammet's head injury) can have a dramatic effect on functionality.
Comment by valerie — February 4, 2008 @ 3:31 pm
February 4th, 2008 at 3:49 pm
This looks like it, bradford - http://www.in-pharmatechnologi...
No idea how it relates to the 'use it or lose it' discussion, but very interesting none-the-less.
Comment by Rob R. — February 4, 2008 @ 3:49 pm
February 4th, 2008 at 5:13 pm
OT: Mike, are you aware of Creationism and Its Critics in Antiquity?
Comment by Mung — February 4, 2008 @ 5:13 pm
February 4th, 2008 at 9:26 pm
Is everyone forgetting about a main point of M.Gene's post?
500 immortal genes.
500 genes "vital for the processes of every cell".
The "most vivid" evidence for natural selection is 500 immortal genes along with some decayed dups.
Am I the only one seeing the point?
Here, 500 immortal genes vital for the processes of every cell, hope this helps.
Comment by BrainyLack — February 4, 2008 @ 9:26 pm
February 4th, 2008 at 10:57 pm
BrainyLack:
Irreducible complexity at the very foundation of life.
Comment by Bradford — February 4, 2008 @ 10:57 pm
February 4th, 2008 at 11:58 pm
great way to put it.
While some commentors are talking about unexpressed dna not being protected by selection pressure they are ignoring what I think is a much bigger issue. these 500 genes. the article says 'They have been preserved intact by selection because most mutations to these would be fatal: if a cell stops working it cannot reproduce'.
I don't completely understand M.Gene's front-loading, but that bit I do understand allows me to see that those duplicate genes not protected by selection pressure really are not a problem for his front-loading and that those 500 genes certainly do help his idea of front-loading.
Comment by BrainyLack — February 4, 2008 @ 11:58 pm
February 5th, 2008 at 12:19 am
BrainyLack:
That tells me cells are not viable without this complex of genes. Of course the answer to that would be that something like a cell, but not quite a cell, was a predecessor and that these precursor cells were able to function with fewer genes than we have identified as essential to cellular function. So natural selection goes back to ground zero despite what we know about cells and the fivehundred. Empirical evidence is powerless when confronted with a willingness to accept imaginary constructs.
Comment by Bradford — February 5, 2008 @ 12:19 am
February 5th, 2008 at 11:43 am
You have empirical evidence that life began de novo, with all 500 genes intact? If not, then all either side has is speculation, about whether a proto-cell (really, a long proto-cell lineage) could exist and if so, what would it's features be?
Comment by One Brow — February 5, 2008 @ 11:43 am
February 5th, 2008 at 3:06 pm
Then argue your point one brow.
Carroll stated the 500 vital genes and he is assuming that archea are primative. If they are derived and those 500 vital genes no longer represent an ancestral but a descended variety then the problem becomes more significant. In all likelihood you will now have to account for more than just 500 vital and necessary genes.
Comment by BrainyLack — February 5, 2008 @ 3:06 pm
February 5th, 2008 at 3:17 pm
My point would be that the question is wide open as to what could or could have happened in the construction of the first cells, and to scoff at one side or the other as using imaginary contstructs to ignore empirical evidence is a prejudicial and untrue accusation.
There is no reason to think that, because a cell seems to require these 500 genes for function, any form of proto-cell would need them all. Given Margulis' work with endosymbiosis, there is even less reason to think one single lineage would need to create all 500 genes on its own.
Comment by One Brow — February 5, 2008 @ 3:17 pm
February 5th, 2008 at 8:06 pm
It's true, it's what you are doing. You are passing the empirical evidence and the straight forward claims of Carroll, which point in the direction of teleology to find an escape route that still allows your philosophical views to be unscathed.
one brow you are forgetting that there are good reasons for believing that archea are derived, not primative. Because of your philosophical views you are assuming that lower end, 500, to be correct. When in fact it could be quite higher.
one brow name these organisms that require less than 500. Or is this were your smoke and mirrors word 'proto-cell' comes into play?
At any rate, you are not denying that all 500 still needed to be in place. You are just dividing that number over 2 or more organisms. 2 or more cells that do not require this vital number of genes.
Comment by BrainyLack — February 5, 2008 @ 8:06 pm
February 5th, 2008 at 10:39 pm
One Brow:
IOW if an imaginary biological construct is proposed it could function with any minimal number of genes. Materialism leads to sterile science.
Comment by Bradford — February 5, 2008 @ 10:39 pm
February 5th, 2008 at 11:17 pm
One Brow:
If I were attempting to make that argument, the fact that cellular function is dependent on the existence of a large number of genes would be a good start in that direction. Cells are palpable. They have definable properties and specified functions with measurable effects. An argument fashioned around cells is one built on scientific data. The alternative precursor cell argument is built on a metaphysical foundation.
Comment by Bradford — February 5, 2008 @ 11:17 pm
February 6th, 2008 at 11:23 am
Possibly even with no genes at all. There are many questions there to explore, as to which smaller groups could form viable communities, how they could arise, interact, etc.
Materialism is a philosophical position. It might inspire some scientists to look in certain direction, much like the design inference might inspire other scientitsts, but it does not lead science. However, to the degree that belief would inspire scientists, it would suggest many worthwhile avenues of research that would be of interest to anyone with an interest in abiogenisis, a few of which I just listed.
Actually, most of the arguments concerning pre-cellular life are based upon the biochemical properties of RNA and its chemical components, as well as other types of materials that were available, from what I can tell. This information is equally available and accepted by a materialsist and a design proponent.
Comment by One Brow — February 6, 2008 @ 11:23 am
February 6th, 2008 at 11:45 am
Your accusation is insulting and untrue. I have made no claims that any poster in here is ignoring evidence, nor scoffed at any position they have, regarding abiogenisis.
It is your view that Carroll's work fits into a notion of design by frontloading, I see no evidence that Carroll shares that interpretation. As far as I am concerned, the question is moot. Front-loading can never be disproven. For example, even if substantial evidence for the existence or pre-cellular life were found, this would do nothing to disrupt the conclusions of the Design Matrix nor to disprove front-loading. Unless I have misunderstood it profoundly, the Design Matrix is not a God-of-the-Gaps arguments you typically see from the IDC crowd.
Well, of course they are derived. They have lineages going back billions of years, just like ours. When biologists refer to an organism as "primitive", they mean it exhibits many of the features they would expect to see in a common ancestor between that life form and some other, less original life form (typically humans).
Well, the number of genes that seem to be "immortal" and universal numbers about 500, according to Carroll. It really matters very little if the first cell needed five hundred, five thousand, or five million genes.
I'm not claiming any of them are or ever will be determined/discovered to have existed. We just don't know, and it is foolish to presume that we do.
Since all forms of life have these 500 "immortal" genes, and these genes code the tasks that all living forms seem to find essential, they appaently needed to be in place in the common ancestry of all forms of cellular life in some fashion.
Well, I doubt we would recognize them as cells. In any case, yes, 2 or more systems of interactions, proto-cells, what have you. Why not?
Comment by One Brow — February 6, 2008 @ 11:45 am
February 6th, 2008 at 1:16 pm
One Brow:
Properties of biologically functional RNA do not support the idea that "precellular life" lies in the pathway to cells.
Comment by Bradford — February 6, 2008 @ 1:16 pm
February 6th, 2008 at 5:03 pm
Well, there seems to be considerable disagreement on this point among people with much better training than I in biochemistry, so I will take this as representing your subjective view only.
Comment by One Brow — February 6, 2008 @ 5:03 pm
February 6th, 2008 at 5:08 pm
There's nothing subjective about properties of mRNA and the functional arrangements of nucleotides. Nor is there evidence of a precellular process leading to this form of RNA and the genetic code enabling its function.
Comment by Bradford — February 6, 2008 @ 5:08 pm
February 6th, 2008 at 5:25 pm
Why the arbitrary limitation to mRNA?
You mean historical evidence, right?
Surely you know there is experimental evidence of the viability. For example,
http://web.mit.edu/newsoffice/...
http://www.sciencedaily.com/re...
We've only begun to see what RNA can do, probably.
Comment by One Brow — February 6, 2008 @ 5:25 pm
February 6th, 2008 at 5:31 pm
From One Brow's link:
Nucleic acids react with nucleotides. We did not need this study to reveal that. The extrapolation indicates the paucity of evidence that cells result from the RNAworld.
Comment by Bradford — February 6, 2008 @ 5:31 pm
February 6th, 2008 at 5:40 pm
So, you quoted the 1998 article when we were just beginning to see what RNA can do, and pretend it's all we know, while overlooking the one in 2001 that shows the discovery of an RNA molecule that can produce copies of other RNA molecules, in effect creating a condition where descent with modification happens? Do you also think we haven't seen anything new in RNA since 2001? Just perhaps, do you think that your statement about what the evidence supports may have been a little hasty?
Comment by One Brow — February 6, 2008 @ 5:40 pm
February 6th, 2008 at 5:50 pm
Bradford:
Hi One Brow. You seem to be fairly new here. In case you hadn't noticed yet, this is a typical Bradford response. If a plausible pathway from self-replicating RNA molecules to proto-cells were ever demonstrated in the lab, I'd wager a hefty sum that Bradford would argue that we already knew that chemicals react with other chemicals and that extrapolation to the actual origin of life would indicate the paucity of evidence bla bla bla.
It's fairly pointless to argue with Bradford, although it can be an entertaining way to kill some time and perhaps convince some lurkers of the emptiness of ID.
Comment by Raevmo — February 6, 2008 @ 5:50 pm
February 6th, 2008 at 9:01 pm
Why not get the empirical evidence that RNA replication leads to cells instead of the RNA world blah, blah, blah we are currently subjected to? I'll wager it does not happen in this millenium.:smile:
Comment by Bradford — February 6, 2008 @ 9:01 pm
February 6th, 2008 at 9:23 pm
OB, it is telling that you believe human languages are not designed while simultaneously believing that OOL data plausibly supports pathways to cells. Raevmo, the emptiness you allude to lies between the ears of ID critics.
Comment by Bradford — February 6, 2008 @ 9:23 pm
February 6th, 2008 at 9:52 pm
Personally, I don't see why the problems of initial conditions and chemical pathways are said to hinder RNA-world speculations. They seem like easy issues for a designer to theoretically get around.
…
Comment by nullasalus — February 6, 2008 @ 9:52 pm
February 6th, 2008 at 11:52 pm
one brow, explain how these RNA segments came to be.
Are you aware of the problems with getting the correct phosphodiester linkages? Aside from the ribonucleotides hitting just that right combination that allows them to make copies, how do you account for the ribonucleotides randomly linking in the correct 3'-5' manner? Considering all of the other chemical reactions that were also available, becoming more and more plausible and eventually trumping this serendipitious random yet consistent 3'-5' phosphodiester linking.
Comment by BrainyLack — February 6, 2008 @ 11:52 pm
February 7th, 2008 at 12:32 am
I don't want to be a wet blanket here, but I would like to raise a couple of issues that bounce off some excerpts from one of the articles linked by One Brow:
Does anyone have an estimate of a) how many thousands of trillions of RNA molecules have been screened (after all, the research is almost 10 years old) thus far and b) what's the best example of a "self-replicator" that has been found? Any references along these lines would be appreciated.
I'm sorry, but I sense confirmation bias here, as Bartel is testing the properties of RNA is a highly artificial (specified) setting. For example, has anyone further tested these reactions to see how robust and resilient they are? It would seem that the next step would be to take the reaction and subject it to different pHs, temps, metal ion concentrations, etc. Heck, does it even work in the context of sterilized sea water? Any references along these lines would be appreciated.
Comment by MikeGene — February 7, 2008 @ 12:32 am
February 7th, 2008 at 12:35 am
Hi null,
LOL
Comment by MikeGene — February 7, 2008 @ 12:35 am
February 7th, 2008 at 11:15 am
Well, here perhaps. I've been discussin topics on Usenet and various websites for close to 10 years, so while not an old hand yet, I have enough experience to know what can and can not be done. It's really not necessary to poison the well against Bradford, nor especially nice.
Comment by One Brow — February 7, 2008 @ 11:15 am
February 7th, 2008 at 11:18 am
No doubt that is a long-term goal.
Well, none of us would be alive to collect on that bet. Considering what science has done in the past 1000 years, though, it seems foolish to bet on what it will or won't do in another 1000.
Comment by One Brow — February 7, 2008 @ 11:18 am
February 7th, 2008 at 11:20 am
Hmmm, I'm not sure I'd say we any solid knowledge yet of "pathways to cells". There is so much yet to uncover. I'm just saying it seems to be a wide-open question, and to accuse anyone on either side of ignoring the evidence is unfair and untrue.
Comment by One Brow — February 7, 2008 @ 11:20 am
February 7th, 2008 at 11:23 am
Absolutely true.
Comment by One Brow — February 7, 2008 @ 11:23 am
February 7th, 2008 at 11:28 am
Nope, I'm not a biochemist, and not aware of any of the details. As I said, there are many professionals who see these issues and find them not insurmountable, and others who think other pathways are more likely. I don't think even the testimony of a few biochemists is enough to say that all the other biochemists are wrong.
So, are you claiming that there is an insurmountable problem? Do you have a link to an annoucement of some peer-reviewed study (if not the sutdy itself) that agrees the problem is insurmountable? I at least provided that much.
Comment by One Brow — February 7, 2008 @ 11:28 am
February 7th, 2008 at 11:39 am
I haven't seen anyting about a self-replicator, but the Science Daily article I linked above talked about an other-replicator discovered in 2001. Put two of those near each other, and you have a replication system. Sel;f-replicators might not even have been in the loop that soon.
That's a good question, and it would need to be addressed before any potential pathway could be seen as a realistic possibility.
Comment by One Brow — February 7, 2008 @ 11:39 am
February 7th, 2008 at 12:14 pm
I'll wager it does not happen in this millenium.
Science is about ascertaining what actually takes place. If a given model is implausible then so be it. That's science.
Comment by Bradford — February 7, 2008 @ 12:14 pm
February 7th, 2008 at 7:18 pm
I think scientists also consider what has happened and what they might be able to do if certain things turn out to be true.
Comment by One Brow — February 7, 2008 @ 7:18 pm
February 8th, 2008 at 1:31 am
Hi One Brow,
Agreed. But what's troubling is that they have had ten years to run such modest experiments.
Comment by MikeGene — February 8, 2008 @ 1:31 am
February 8th, 2008 at 11:41 am
MikeGene,
Are you sure that's true? For example, some of the later theories have proto-like organizing on mica leaves for just that reason, protection.
Comment by One Brow — February 8, 2008 @ 11:41 am