De novo origination of a gene encoding a functional protein

Posted 14 June 2008 by Arthur Hunt

A recurrent theme amongst ID proponents is the supposed difficulty of protein evolution, especially as it relates to the origination of new protein-coding genes. This is, I suspect, a key reason why ID proponents such as Paul Nelson are so enamoured of ORFans, and a foundational principle for the application of ID theory to evolution (the idea being that protein-coding genes are possessed of Complex Specified Information, and thus cannot arise by natural processes). Thus, studies that pertain to the origins of new protein-coding genes are going to factor largely in the scientific aspect of the ID debate, especially since ID proponents insist that new protein-coding genes cannot arise “by chance”. It is in this context that a recent study by Jing Cai and colleagues is of interest. The title of the article suffices to explain the study – “De novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae”. What these authors describe is a series of studies of a yeast gene, BSC4. This gene was originally identified as a candidate containing a so-called read-through translation termination (or stop) codon. This gene was studied in more depth, whereupon Cai et al. found that the protein encoded by this gene was novel in genome databases, not resembling any other protein in any organism. Importantly, this includes the genomes of related Saccharomyces species; this indicates that this protein in S. cerevisiae arose relatively recently, after this species diverged from its close relatives. Of course, all of these results are the outcomes of “sequence-gazing” – compilation and analysis of genome sequence datasets. Cai et al. determined to test whether BSC4 was a true protein-coding gene, or just an unexpressed sequence that just happens to contain an open-reading frame. To this end, Cai et al. performed a number of studies:

They analyzed the BSC4 coding region in a number of S. cerevisiae isolates, and found evidence for purifying selection amongst these genes. (In other words, they found that non-synonymous, or amino acid-changing, mutations were fixed much less frequently than synonymous mutations.) This result is expected if the gene is expressed as protein (and, of course, if the protein has a function that is acted upon by natural selection).
To buttress this conclusion, these authors then searched databases of peptides (1) obtained by tandem mass spectrometry (MS/MS) analysis of yeast proteins; this effort yielded 29 peptides that corresponded to the BSC4 gene. This is strong evidence for the proposition that the BSC4 gene is expressed as protein, as this is the only way that these peptides could be found in MS/MS studies.
That the BSC4 gene is expressed as RNA was confirmed by reverse transcription/polymerase chain reaction (RT/PCR) studies.
Finally, these authors noted that a systematic screen for synthetic lethality indicated genetic interactions between BSC4 and both DUN1 and RPN4, two other yeast proteins. As with the MS/MS and RT/PCR studies, synthetic lethality is best explained if the two partners are both expressed as proteins.

As a package, these results make a very compelling case that the BSC4 gene is expressed as protein, AND that it has some biological function.

What then of the matter of the origins of the BSC4 gene? The following bullets summarize some pertinent items.

Fig. 3A from the paper (reproduced below) shows the arrangement of the BSC4 gene in S. cerevisiae, and the corresponding genetic locus from six close relatives. It also shows that this region is a recent development, as it is absent from more distantly-related fungi (Ylip. Ncra, and Spom at the bottom of the figure). This figure describes the history of the locus – it arose via some sort of rearrangement sometime before the seven yeast species diverged from one another, but after they diverged from other fungal lineages. (Importantly, the BSC4 gene did not “come from” another pre-existing protein-coding gene, either in yeast or any other organism. This argues against horizontal gene flow and/or gene duplication as a source of the BSC4 protein-coding region.)
In those different species (S. bayanus, S. paradoxus, etc.) that possess the same locus that contains BSC4 in S. cerevisiae, there is considerable nucleotide sequence divergence, more than is usually seen in protein-coding genes. However, there is a degree of conservation consistent with a function for this region in these yeast species as encoding so-called non-coding RNAs.
There is a ca. 100 bp portion of the BSC4 gene that is about 50% identical amongst four different yeast species (S. bayanus, S. mikatae, S. paradoxus, and S. cerevisiae). This extended region of identity in four species strongly suggests that the region of interest existed in the common ancestor of the four species. This is important, as it means that the BSC4 gene did not arise by some other insertion, duplication, or rearrangement; rather, it is the product of the accumulation of point mutations.
This region is transcribed (as determined by RT/PCR analysis) in these four species. This supports the proposition that these regions encode non-coding RNAs.

Putting these observations together, it is apparent that the LYP1-ALP1 region (including the intergenic region of interest) in yeasts arose by a rearrangement that produced these two genes and an intergenic region that is transcribed but (except for S. cerevisiae) has no protein-coding potential. At some point after this founding rearrangement, and after the S. cerevisiae lineage diverged from the other yeast lineages, part of the intergenic region picked up translation initiation and termination codons (one of which is leaky, the property that allowed the identification of BSC4 in the first place). The result was a new protein-coding region (BSC4), the product of which either possessed from the outset or gained, via additional mutation, the functions inferred by the synthetic lethality results.

(While this issue is not discussed at much length, I suspect that the authors would argue that de novo origination is a better explanation than gene loss in this case, since the latter would invoke gene loss in at least six yeast species. This rather high rate of loss is not consistent with the observation that different geographic isolates of S. cerevisiae, many of which have been isolated for millennia, all retain the BSC4 gene.) Finally, it is of interest to note that the antecedent of BSC4 gene in other yeast species seems to encode so-called non-coding RNAs. This raises the interesting possibility that non-coding RNAs may be sources of novel protein-coding genes, and suggests that one step of a hypothetical pathway for the de novo origination of new proteins - the "creation" of transcription regulatory sequences - may not be an issue (or at least a conceptual hurdle of any import). Also, it helps to point out the BSC4 region does not seem to be RRP6-dependent (see this essay), and thus the BSC4 is not derived from these so-called Cryptic Unstable Transcripts Footnote: (1) A fairly new approach to studying genomes and their encoded products is to isolate collections of proteins by various means, digest them (or chop them up) with proteases such as trypsin, and then analyze the peptides by tandem mass spec-mass spec (MS/MS). MS/MS provides, among other things, the exact (to the hydrogen atom) atomic mass of the peptide; combined with good calculators, it is possible to assign a unique amino acid sequence to most such masses. Thanks to amazing advances in the hardware, it’s possible to perform this with complex mixtures (such as crude lysates) and get an idea of the scope of the expressed proteins in a compartment or cell. Cai et al. refer to such collections in their paper. An overview of the approach is here and the database is here. Reference for Cai et al: Cai J, Zhao R, Jiang H, Wang W. 2008. De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae. Genetics 179, 487-496. A slightly different version may also be found at The RNA Underworld.

41 Comments

Frank B · 14 June 2008

If Michael Behe can twist the "E. Coli Evolving Citrate Utilization" study to support ID, this study is a piece of cake. But otherwise, seeing real scientists doing real science is so refreshing.

hje · 14 June 2008

Can't wait until Behe's glib dismissal of the results on his Amazon blog: "Trivial non-finding." or "ID predicts just that."

fnxtr · 14 June 2008

So now I'm wondering if non-coding RNA's may have some other function, just like a lot of non-coding DNA does.

Clearly, fnxtr has lots of Googling to do...

Once again the difference between scientists and liars is made clear. Scientists do the work... and cue liars misrepresenting someone else's work in 3, 2....

raven · 14 June 2008

wikipedia nylon eating bacteria: Scientists were able to induce another species of bacteria, Pseudomonas aeruginosa, to evolve the capability to break down the same nylon byproducts in a laboratory by forcing them to live in an environment with no other source of nutrients. The P. aeruginosa strain did not seem to use the same enzymes that had been utilized by the original Flavobacterium strain.[2] Other scientists were able to get the ability to generate the enzymes to transfer from the Flavobacterium strain to a strain of E.Coli bacteria via a plasmid transfer.[3] Genetic analysis of the plasmid led some scientists to the conclusion that the genes to produce one of the enzymes had most likely resulted from the combination of a gene duplication event with a frame shift mutation.[4] Further analysis has led to speculation that the fact that the frame shift was able to produce a functioning enzyme was related to the absence of stop codons in the duplicate gene.[5] Research has continued in the hope of better understanding the mechanisms involved in the evolution of new enzymes, and because of the possible value of bacteria that can metabolize man made molecules to toxic waste cleanup.

A few more examples of de novo evolution of new genes. Nylon eating bacteria of course. A frameshift within an existing gene created a new enzyme activity capable of eating a novel substrate, nylon. The T cytoplasmic sterility trait in corn, which was explained at length by Arthur Hunt, the current poster here on PT a while back. We know that evolution can create new information because we see it happen. So much for the creos.

Frank J · 14 June 2008

Can’t wait until Behe’s glib dismissal of the results on his Amazon blog: “Trivial non-finding.” or “ID predicts just that.”
— hje

It's virtually guaranteed that both will be claimed by the ID community, even if Behe, or any other ID individual, just picks one and sticks to it. But that's perfectly understandable because ID only predicts "trivial non-findings." While individual IDers may have learned not to pretend that evolution is unfalsifiable and falsified at the same time, the movement as a whole has consistently shown that it will use whatever rhetorical tool it can, regardless of how inconsistent.

Torbjörn Larsson. OM · 14 June 2008

Yes, thanks for some refreshing weekend science results.

On Behe: don't begrudge him his goal post moving, it makes him score self goals so often. (Astrology. Pfff ... he he he.)

djlactin · 15 June 2008

Interesting paper (or summary thereof), but I see a potential hole (which you have noticed also): I think this result definitely suggests de novo origin of a coding gene; I simply don't accept that the evidence is strong enough to state categorically that it has occurred. This is the point that caught my attention:

This region is transcribed (as determined by RT/PCR analysis) in these four species. This supports the proposition that these regions encode non-coding RNAs.

(I think you mean 'six species') Your analysis was:

(While this issue is not discussed at much length, I suspect that the authors would argue that de novo origination is a better explanation than gene loss in this case, since the latter would invoke gene loss in at least six yeast species. This rather high rate of loss is not consistent with the observation that different geographic isolates of S. cerevisiae, many of which have been isolated for millennia, all retain the BSC4 gene.)

(Italics mine.) First: the observation that other yeasts transcribe but do not translate the region puzzles me. I see two explanations (1) that untranslated RNA transcripts could have some function (not easily dismissed out-of-hand); (2) this transcription is a physiological fossil of a protein that has lost function in relatively recent evolutionary time. The second possibility is what caught my eye. You suggested how the authors might use Ockham's razor to reject the alternative hypothesis of multiple function loss in related species. Aside from your putting words in the authors' mouths, here is where I object: Ockham's razor functions by parsimony, which is not necessarily equivalent to 'counting changes'. One de novo gain of function vs as many as six losses of function: which is more likely? Your assessment that 'gain of function' is a "better explanation" of the results than 'loss of function' seems too facile. First: your assessment that absence of the functional gene in the other species requires 6 losses does not necessarily follow from the results that you summarize. The number depends on the topology of the cladogram of relationships between the species; it could be as little as one (if S. cerevisiaea is the basal member of a clade that includes all of the others, one loss in the "other group" after it diverged is sufficient) or two (if S. cerevisiae/S. bayanus is a natural grouping and the others form a natural clade). Second: considering that losses of function are relatively simple, but that gain of function is not, you are not applying appropriate weighting to the possibilities. Third: I do not know what the 'ecologies' of the non-Saccharomyces species are. Are they also Sugar -> Ethanol fermenters? ( S. cerevesiae is a beer yeast; S. bayanus is a champagne yeast.) If not, simple comparisons of genomes may be misguided. Fourth: Isolation of S. cerevesiae "for millennia" and the apparent lack of diversity at this locus, is irrelevant to this argument. As a domesticated species, it has been subjected to selection for its ability to produce alcohol. Purifying selection, I wager. Perhaps you are correct that one de novo origin is more likely than six losses (I remain skeptical), but even a less-likely possibility is still a possibility, and to reject it, you need data. Hand-waving does not suffice. This was an interesting and suggestive paper. I simply remain skeptical that the data as presented demonstrate convincing evidence for de novo origin of a protein. IMHO, more work is necessary to 'prove' this beyond reasonable doubt. "Extraordinary claims require extraordinary evidence." - Carl Sagan

Philip Bruce Heywood · 15 June 2008

I am going to attempt to bring some of these contributors at least up to speed with a few of the Ancient Greeks. It could be a monumental task.

Raven, for example, writes, "We know that evolution can create new information ...... ."

Now, Socrates; is a gene a device that carries/is coded with information? Is your answer in the affirmative?

Where did at least some of the information that influenced the coding of this device come from? The environment? Affirmative?

So, you have an information device that encounters a form of information - correct? You don't mean that the gene made up its own information, do you? No, you mean it encountered something that had an informative outcome - correct?

For an information codeable device to increase the quantity of information it contains, must it be able to read the information that is being added to it? Put it this way: for you to impart information to your desktop computer, do you feed info. into it via a keyboard or some such device that renders your information compatible with the information storage capability of the computer? You don't merely kick it and speak French?

So the information imparted from the environment/Nature was necessarily readable by the organism, wasn't it? Correct?

So what do you mean by, "Evolution can create ..... ?"

You're not getting confused with that other E word, are you --Elvis?

Perhaps you meant, "There is a mechanism in Nature, by which information can be added to the information storage/carrying devices of living organisms?"

Divalent · 15 June 2008

Jeeze-louise, Heywood.

Do you really think you are constructing logical arguments? If so, instead of just sitting around and practicing sophistry, why don't you just take the next logical step and do the work? If you are right, it shouldn't be hard, and I promise you will get a Nobel prize.

paul flocken · 15 June 2008

Unfortunately for Heywood, the first person to discover that mechanism was Darwin, not Jesus, and the mechanism he discovered was natural selection (though there are others) and not the 'word of god'(or would that be, according to Dembski, the logos of john).

fnxtr · 15 June 2008

(sigh) Variations (which may have been influenced by environment) which better suit the environment are not the same as insertions by the environment, Phil. Maybe you should lay off the LSD for a while.

David Stanton · 15 June 2008

So let's review shall we:

No beneficial mutations can occur: WRONG

No new genes or functions can arise: WRONG

No increase in information can occur: WRONG

Why would anyone listen to anything these guys have to say ever again? Why don't they at least raad the scientific literature if they can't be bothered to do any research?

Stanton · 15 June 2008

David Stanton said: Why would anyone listen to anything these guys have to say ever again? Why don't they at least read the scientific literature if they can't be bothered to do any research?

Maybe because they don't know how to do either research or experimentation, and that they have absolutely no drive what so ever to learn anything, let alone learning how to do either research or experimentation?

Scott · 15 June 2008

Stanton said:
We know that evolution can create new information because we see it happen.

PBH said:
Perhaps you meant, “There is a mechanism in Nature, by which information can be added to the information storage/carrying devices of living organisms?”

Um, yes, that is exactly what he said. That mechanism is "evolution". Your point? Unfortunately for your "argument", living organisms do in fact respond to the environment, rather than simply store information placed there by external actors.

Philip Bruce Heywood · 15 June 2008

My point, which is obvious to anyone with an understanding of the principles of logic and of science, is that this "Evolution" that can "create" is at least as divine as Elvis or a medieval Pope (is there much difference between the two, in some circles?)whereas the mechanisms which were the engines of evolution have no divinity nor connotations of supernatural ability whatsoever.

To say that a process of Nature can create new information is to overthrow the basis of science. Matter can be neither created nor destroyed. Information is intrinsical to matter itself. The position of an electron in orbit is an item of information in its own right. That's how come a few fistfulls of matter flattened Hiroshima. Information/organization is hugely significant in physical chemistry.

All this trumpet blow of the organizational powers of this omniscient and omnipresent "Evolution" is enough to give Socrates a bellyache.

PvM · 15 June 2008

To say that a process of Nature can create new information is to overthrow the basis of science.

Not at all. Matter and information should not be confused as some seem to do. More foolishness from my friend PBH, what's next?

PvM · 15 June 2008

Information is indeed incredibly relevant and contrary to those less informed, information an be shown to trivially increase under selective processes and variation.

Tom Schneider, Chris Adami, Lenski and others have shown that this is indeed the case.

So why do we here PBH suggest otherwise? I guess because he lack familiarity with the topic and the research in these areas.

Stephen Wells · 16 June 2008

It's very amusing to see PBH claim that matter can't be created or destroyed. More than a hundred years out of date there. He even seems to think that hiroshima was destroyed by a chemical explosive. Pitiful ignorance.

Fantastic research result here, shame about the trolling.

bigbang · 16 June 2008

djlactin says: "I simply remain skeptical that the data as presented demonstrate convincing evidence for de novo origin of a protein. IMHO, more work is necessary to ‘prove’ this beyond reasonable doubt."

Agreed.

Philip Bruce Heywood · 16 June 2008

I have attempted to put a few thoughts together (published via my site) - not being one for being able to comprehend Pauli vector, Planck constant, Fourier transform, and nor even Schor's algorithm, I am obliged to leave such sorceries and incantations to the relevant wizards. The square root of negative one gives me dispepsia to this day. It's worse than having treacle in your hair, just trying to think about it.

Fortunately we have modern science, which is coming along very nicely with the relevant advances that clearly show the mechanisms of evolution, if not in fine detail as yet, at least in broad outline. Elvis doesn't rate a mention.

I'll take the liberty of reminding the gentle Reader of the definition of Science. Science describes the natural universe. That universe in which no new matter is being created. The same universe in which all natural processes and procedures are governed by immutable laws.

Since science describes that which exists, someone or something thought it all through before science describes it. Otherwise, it wouldn't exist. Even Einstein thought of nothing new. He described that which exists. All information exists independent of whether I can think of it, or not. Writing information into a gene does not make the information novel. The gene, conceivably, could be novel. Apply Socrates.

Allen MacNeill · 16 June 2008

PBH fundamentally misunderstands the nature of information. Yes, as far as we can tell it is the case that information cannot exist without matter and energy, but it is just as clearly not the case that it can reduced to one or the other. On the contrary, as Gregory Bateson and others have shown, information consists of a relationship between material objects, mediated by a transformation of energy. Furthermore, although it is the case that energy and matter can be transformed into each other (via Einstein's energy/matter equivalence law), neither energy nor matter can be converted into information, nor vice versa. Translated, yes; converted no.

Claude Shannon showed the relationship between information and energy almost a half century ago, and Norbert Weiner et al showed how information in recursive relationships could modify cause-effect relationships at about the same time. What seems relevant, based on what we understand now about the relationship between energy, matter, and information, is that meaningful information always involves a translation from one medium to another (as in the translation of base sequences in mRNA into amino acid sequences in polypeptides). As far as we can tell, such translation processes are always accompanied by in increase in entropy/decrease in free energy, and so the origin and/or transfer of meaningful information is tied to thermodynamics (and, of course, requires material vehicles for encoding/decoding). But to claim that information is directly transformable into either energy or matter is falsified by every empirical observation we have made about the relationships between energy, matter, and information.

JGB · 16 June 2008

A quick way to encapsulate the on going misrepresentation of "information" would be to set-up two experiments. One would be a simplified environment with say a mating pair of organisms. Now before the start of the experiment we have no idea about the fitness of the organisms (yes this is a bad evolutionary model). In the second experiment we have two randomly betting computer programs playing Texas holdem (poker). According to the often proffered "definition" of information neither experiment could yield information. Of course we know in both cases we do get out real information, the winner and the reproductive success of the mating pair.

A programmer could even craft an evolutionary betting algorithm I'd imagine and the computer could teach itself which hands to bet based only on the results with no knowledge in the betting program of which hands are best.

fnxtr · 16 June 2008

Since science describes that which exists, someone or something thought it all through before science describes it. Otherwise, it wouldn’t exist. Even Einstein thought of nothing new. He described that which exists. All information exists independent of whether I can think of it, or not. Writing information into a gene does not make the information novel. The gene, conceivably, could be novel. Apply Socrates.

Okay, that's just garbage, Phil. I think you took Mark Hausam's "Universe, therefore God" idiocy a little too seriously. There is no "writing information into a gene", there are only imperfect replications which lead to greater or lesser fitness, or benign changes in the base sequences. Your teleology is just another fairy story.

ndt · 16 June 2008

Philip Bruce Heywood said: Since science describes that which exists, someone or something thought it all through before science describes it. Otherwise, it wouldn't exist.

Your conclusion doesn't follow from your premises.

paul flocken · 16 June 2008

Philip Bruce Heywood said: intrinsical

snicker

Chayanov · 16 June 2008

To say that a process of Nature can create new information is to overthrow the basis of science.

What, like when a sperm fertilizes an egg to create a genetically unique individual?

hje · 16 June 2008

Pi times Planck's constant tells us that the curvature of the multiverse must be undefined, therefore we must calculate the intrinsic energy density of the quark gluon plasma, which according to quantum chromodynamics is undefined with respect to Hawking specified information content of a rotating black hole singularity, with the exception that quantum loop gravity permits a violation Shannon's postulates due to Bell's inequality. Apply Wittgenstein, unless Sartre is more relevant.

See, we all can string smart sounding words and phrases together that mean absolutely nothing. Ain't no big-ee.

fnxtr · 16 June 2008

"Apply to affected area" springs to mind...

Philip Bruce Heywood · 16 June 2008

hje said: Pi times Planck's constant tells us that the curvature of the multiverse must be undefined, therefore we must calculate the intrinsic energy density of the quark gluon plasma, which according to quantum chromodynamics is undefined with respect to Hawking specified information content of a rotating black hole singularity

Yeah, my son's bicycle got a flat rear tyre that had to be repaired, too.

Philip Bruce Heywood · 16 June 2008

Chayanov said:
To say that a process of Nature can create new information is to overthrow the basis of science.
What, like when a sperm fertilizes an egg to create a genetically unique individual?

Individuality in terms of genetics is the product of permutations and combinations acting on available information. I won't be a heretic and say it is blind chance - blind chance is a very difficult concept. I suspect that there is much more to the genetic outcome of fertilization than pure chance permutations and combinations. Employing an inferior analogy - poker machines come up with a brand new payout with monotonous regularity. This is achieved through statistical outcomes, not through creation of new information.

Mike Elzinga · 16 June 2008

PBH really needs to link up with Joe Newman. These two like-minded geniuses would really get along like two peas in a pod. The result could be the combining of PBH’s “superconduction plus the Earth, Moon, Sun gravitational system which imparts information to photons” and Joe Newman’s “gyroscopic spin particles” by which he gets energies the size of E = mc² in the following manner:

The GYROSCOPIC SPIN of the "gyroscopic massergies" (descriptive terminology for the spinning fundamentals which are the equivalent of both mass and energy) is the important aspect of their physical, mechanical behavior.

Just think; unlimited energy from Joe Newman that is enhanced with the information provided by Philip Bruce Heywood’s deep insights into “technology”. Smart Energy! And they are both experts on thermodynamics as one can easily see by studying both their websites. PBH knows all about “entropy barriers” and Joe Newman knows how to get more energy out of a machine than is put in without violating the Laws of Thermodynamics. (Be careful when you read; just viewing such genius hurts the brains of ordinary mortals.) Breathtaking!!! One rarely gets to see two supernovas occurring simultaneously! Imagine the brilliance of the merger!

PvM · 16 June 2008

bigbang said: djlactin says: "I simply remain skeptical that the data as presented demonstrate convincing evidence for de novo origin of a protein. IMHO, more work is necessary to ‘prove’ this beyond reasonable doubt." . Agreed.

And yet Bigbang still hopes that science will be able to show evidence of the supernatural. And of course, reasonable doubt in some people's hands will raise the bar unnecessarily high to avoid the obvious.

PvM · 16 June 2008

Individuality in terms of genetics is the product of permutations and combinations acting on available information. I won’t be a heretic and say it is blind chance - blind chance is a very difficult concept. I suspect that there is much more to the genetic outcome of fertilization than pure chance permutations and combinations.

So what about blind chance and selection? No wonder that the square root of -1 confuses you PBH.

Ex-drone · 17 June 2008

I used to marvel that you could create matter out of energy. Now, PBH sets us straight. It's not energy; it's pre-existing matter. Einstein probably expended a lot of effort coming up with E = mc², but I guess he need not have bothered. PBH shows us that science is easier to do if you just declare things to be so.

bigbang · 17 June 2008

PvM claims: “And yet Bigbang still hopes that science will be able to show evidence of the supernatural.”

How utterly dishonest. As PvM surely knows, nowhere have I said or suggested such nonsense.

Apparently PvM’s “supernatural” “Christian God” “hidden” in a “permanent gap of ignorance” doesn’t require any sort of intellectual honesty. Earth to PvM----your god, like your above accusation, is a delusion and/or a lie; and reinforces P Z Meyers’s contention that religion itself is a lie and a danger.

fnxtr · 17 June 2008

Everyone knows it was hyperintelligent pandimensional beings.

Stanton · 17 June 2008

So, can someone explain how ~~bigbang~~Bigot's continued, and continuously incompetent attempts at assassinating PvM's (and all other Christians who accept evolution) is directly germane to the topic of a functional gene product arising de novo?

It is the only thing that this moronic bigot can talk about on every thread he infests.

sylvilagus · 17 June 2008

Philip Bruce Heywood said:
Chayanov said:
To say that a process of Nature can create new information is to overthrow the basis of science.
What, like when a sperm fertilizes an egg to create a genetically unique individual?
Individuality in terms of genetics is the product of permutations and combinations acting on available information. I won't be a heretic and say it is blind chance - blind chance is a very difficult concept. I suspect that there is much more to the genetic outcome of fertilization than pure chance permutations and combinations. Employing an inferior analogy - poker machines come up with a brand new payout with monotonous regularity. This is achieved through statistical outcomes, not through creation of new information.

You clearly do not understand any (of the several) definitions of information. Here's a question for you: do you really think that you have the knowledge and understanding to make the pronouncements that you do? Time after time, you assert, without evidence, the most mind-bogglingly wrong claims about basic science. Then, when corrected, you never lsiten, but intead go away or retreat into techno-babble: Why do you do this? I'm serious. I come to this site to gain education about evolutionary biology. I've tried in the apst to engage you in thougtful discussion as have others, and each time the result is the same... do you really not see how immaturely and ignorantly you are acting to those of us who sicnerely want to learn and discuss? Or are you itnentionally just trying to annoy people?

slang · 18 June 2008

sylvilagus said to PBH: Here's a question for you: do you really think that you have the knowledge and understanding to make the pronouncements that you do? Time after time, you assert, without evidence, the most mind-bogglingly wrong claims about basic science.

"Ignorance more frequently begets confidence than does knowledge" -- Charles Darwin

caynazzo · 30 June 2008

Evidence of mRNA is not evidence of proteins. Westerns and antibody staining is where it's at.

Arthur Hunt · 30 June 2008

Hi caynazzo,

I agree with you. However, Cai et al. provide pretty compelling evidence that the BSC4 gene is expressed as protein. This evidence is the mass spec data, as I discuss in the essay.